316 results on '"A. Scarsbrook"'
Search Results
2. Toxicity Prediction in Pelvic Radiotherapy Using Multiple Instance Learning and Cascaded Attention Layers
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Behnaz Elhaminia, Alexandra Gilbert, John Lilley, Moloud Abdar, Alejandro F. Frangi, Andrew Scarsbrook, Ane Appelt, and Ali Gooya
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Health Information Management ,Health Informatics ,Electrical and Electronic Engineering ,Computer Science Applications - Published
- 2023
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3. Diagnostic Accuracy of a Convolutional Neural Network Assessment of Solitary Pulmonary Nodules Compared With PET With CT Imaging and Dynamic Contrast-Enhanced CT Imaging Using Unenhanced and Contrast-Enhanced CT Imaging
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Jonathan R. Weir-McCall, Elise Debruyn, Scott Harris, Nagmi R. Qureshi, Robert C. Rintoul, Fergus V. Gleeson, Fiona J. Gilbert, Anindo Banerjee Lucy Brindle, Matthew Callister, Andrew Clegg, Andrew Cook, Kelly Cozens, Philip Crosbie, Sabina Dizdarevic, Rosemary Eaton, Kathrin Eichhorst, Anthony Frew, Ashley Groves, Sai Han, Jeremy Jones, Osie Kankam, Kavitasagary Karunasaagarar, Lutfi Kurban, Louisa Little, Jackie Madden, Chris McClement, Ken Miles, Patricia Moate, Charles Peebles, Lucy Pike, Fat-Wui Poon, Donald Sinclair, Andrew Shah, Luke Vale, Steve George, Richard Riley, Andrea Lodge, John Buscombe, Theresa Green, Amanda Stone, Neal Navani, Robert Shortman, Gabriella Azzopardi, Sarah Doffman, Janice Bush, Jane Lyttle, Kenneth Jacob, Joris van der Horst, Joseph Sarvesvaran, Barbara McLaren, Lesley Gomersall, Ravi Sharma, Kathleen Collie, Steve O’Hickey, Jayne Tyler, Sue King, John O’Brien, Rajiv Srivastava, Hugh Lloyd-Jones, Sandra Beech, Andrew Scarsbrook, Victoria Ashford-Turner, Elaine Smith, Susan Mbale, Nick Adams, and Gail Pottinger
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Pulmonary and Respiratory Medicine ,Cardiology and Cardiovascular Medicine ,Critical Care and Intensive Care Medicine - Abstract
Solitary pulmonary nodules (SPNs) measuring 8 to 30 mm in diameter require further workup to determine the likelihood of malignancy.What is the diagnostic performance of a lung cancer prediction convolutional neural network (LCP-CNN) in SPNs using unenhanced and contrast-enhanced CT imaging compared with the current clinical workup?This was a post hoc analysis of the Single Pulmonary Nodule Investigation: Accuracy and Cost-Effectiveness of Dynamic Contrast Enhanced Computed Tomography in the Characterisation of Solitary Pulmonary Nodules trial, a prospective multicenter study comparing the diagnostic accuracy of dynamic contrast-enhanced (DCE) CT imaging with PET imaging in SPNs. The LCP-CNN was designed and validated in an external cohort. LCP-CNN-generated risk scores were created from the noncontrast and contrast-enhanced CT scan images from the DCE CT imaging. The gold standard was histologic analysis or 2 years of follow-up. The area under the receiver operating characteristic curves (AUC) were calculated using LCP-CNN score, maximum standardized uptake value, and DCE CT scan maximum enhancement and were compared using the DeLong test.Two hundred seventy participants (mean ± SD age, 68.3 ± 8.8 years; 49% women) underwent PET with CT scan imaging and DCE CT imaging with CT scan data available centrally for LCP-CNN analysis. The accuracy of the LCP-CNN on the noncontrast images (AUC, 0.83; 95% CI, 0.79-0.88) was superior to that of DCE CT imaging (AUC, 0.76; 95% CI, 0.69-0.82; P = .03) and equal to that of PET with CT scan imaging (AUC, 0.86; 95% CI, 0.81-0.90; P = .35). The presence of contrast resulted in a small reduction in diagnostic accuracy, with the AUC falling from 0.83 (95% CI, 0.79-0.88) on the noncontrast images to 0.80 to 0.83 after contrast (P .05 for 240 s after contrast only).An LCP-CNN algorithm provides an AUC equivalent to PET with CT scan imaging in the diagnosis of solitary pulmonary nodules.ClinicalTrials.gov Identifier; No.: NCT02013063.
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- 2023
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4. A Road Map for Designing Phase I Clinical Trials of Radiotherapy–Novel Agent Combinations
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Brown, Sarah R, Hinsley, Samantha, Hall, Emma, Hurt, Chris, Baird, Richard D, Forster, Martin, Scarsbrook, Andrew F, Adams, Richard A, Brown, Sarah R [0000-0002-7975-7537], Hinsley, Samantha [0000-0001-6903-4688], Hall, Emma [0000-0001-5999-5020], Hurt, Chris [0000-0003-1206-8355], Baird, Richard D [0000-0001-7071-6483], Scarsbrook, Andrew F [0000-0002-4243-032X], Adams, Richard A [0000-0003-3915-7243], and Apollo - University of Cambridge Repository
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Cancer Research ,Clinical Trials, Phase I as Topic ,Dose-Response Relationship, Drug ,Maximum Tolerated Dose ,Oncology ,Research Design ,Neoplasms ,Antineoplastic Combined Chemotherapy Protocols ,Humans ,Software - Abstract
Radiotherapy has proven efficacy in a wide range of cancers. There is growing interest in evaluating radiotherapy–novel agent combinations and a drive to initiate this earlier in the clinical development of the novel agent, where the scientific rationale and preclinical evidence for a radiotherapy combination approach are high. Optimal design, delivery, and interpretation of studies are essential. In particular, the design of phase I studies to determine safety and dosing is critical to an efficient development strategy. There is significant interest in early-phase research among scientific and clinical communities over recent years, at a time when the scrutiny of the trial methodology has significantly increased. To enhance trial design, optimize safety, and promote efficient trial conduct, this position paper reviews the current phase I trial design landscape. Key design characteristics extracted from 37 methodology papers were used to define a road map and a design selection process for phase I radiotherapy–novel agent trials. Design selection is based on single- or dual-therapy dose escalation, dose-limiting toxicity categorization, maximum tolerated dose determination, subgroup evaluation, software availability, and design performance. Fifteen of the 37 designs were identified as being immediately accessible and relevant to radiotherapy–novel agent phase I trials. Applied examples of using the road map are presented. Developing these studies is intensive, highlighting the need for funding and statistical input early in the trial development to ensure appropriate design and implementation from the outset. The application of this road map will improve the design of phase I radiotherapy–novel agent combination trials, enabling a more efficient development pathway.
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- 2022
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5. Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus)
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Tom Oosting, Lourdes Martínez-García, Giada Ferrari, Alexander J. F. Verry, Lachie Scarsbrook, Nicolas J. Rawlence, Maren Wellenreuther, Bastiaan Star, and Peter A. Ritchie
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Phylogeography ,Nucleotides ,Genome, Mitochondrial ,Genetics ,Humans ,Genetic Variation ,DNA, Mitochondrial ,Phylogeny ,Genetics (clinical) - Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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- 2022
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6. IMPACT-Global Hip Fracture Audit: Nosocomial infection, risk prediction and prognostication, minimum reporting standards and global collaborative audit
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Andrew J. Hall, Nicholas D. Clement, Cristina Ojeda-Thies, Alasdair MJ. MacLullich, Giuseppe Toro, Antony Johansen, Tim O. White, Andrew D. Duckworth, Hani Abdul-Jabar, Rashid Abu-Rajab, Ahmed Abugarja, Karen Adam, Héctor J. Aguado Hernández, Gedeón Améstica Lazcano, Sarah Anderson, Mahmood Ansar, Jonathan Antrobus, Esteban Javier Aragón Achig, Maheswaran Archunan, Mirentxu Arrieta Salinas, Sarah Ashford–Wilson, Cristina Assens Gibert, Katerina Athanasopoulou, Mohamed Awadelkarim, Stuart Baird, Stefan Bajada, Shobana Balakrishnan, Sathishkumar Balasubramanian, James A. Ballantyne, Leopoldo Bárcena Goitiandia, Benjamin Barkham, Christina Barmpagianni, Mariano Barres-Carsi, Sarah Barrett, Dinnish Baskaran, Jean Bell, Katrina Bell, Stuart Bell, Giuseppe Bellelli, Javier Alberto Benchimol, Bruno Rafael Boietti, Sally Boswell, Adriano Braile, Caitlin Brennan, Louise Brent, Ben Brooke, Gaetano Bruno, Abdus Burahee, Shirley Burns, Giampiero Calabrò, Lucy Campbell, Guido Sebastian Carabelli, Carol Carnegie, Guillermo Carretero Cristobal, Ethan Caruana, M.a Concepción Cassinello Ogea, Juan Castellanos Robles, Pablo Castillon, Anil Chakrabarti, Antonio Benedetto Cecere, Ping Chen, Jon V. Clarke, Grace Collins, Jorge E. Corrales Cardenal, Maurizio Corsi, Gara María Cózar Adelantado, Simon Craxford, Melissa Crooks, Javier Cuarental-García, Rory Cuthbert, Graham Dall, Ioannis Daskalakis, Annalisa De Cicco, Diana de la Fuente de Dios, Pablo Demaria, John Dereix, Julian Díaz Jiménez, José Luis Dinamarca Montecinos, Ha Phuong Do Le, Juan Pablo Donoso Coppa, Georgios Drosos, Andrew Duffy, Jamie East, Deborah Eastwood, Hassan Elbahari, Carmen Elias de Molins Peña, Mamoun Elmamoun, Ben Emmerson, Daniel Escobar Sánchez, Martina Faimali, Maria Victòria Farré-Mercadé, Luke Farrow, Almari Fayez, Adam Fell, Christopher Fenner, David Ferguson, Louise Finlayson, Aldo Flores Gómez, Nicholas Freeman, Jonathan French, Santiago Gabardo Calvo, Nicola Gagliardo, Joan Garcia Albiñana, Guillermo García Cruz, Unai García de Cortázar Antolín, Virginia García Virto, Sophie Gealy, Sandra Marcela Gil Caballero, Moneet Gill, María Soledad González González, Rajesh Gopireddy, Diane Guntley, Binay Gurung, Guadalupe Guzmán Rosales, Nedaa Haddad, Mahum Hafeez, Petra Haller, Emer Halligan, John Hardie, Imogen Hawker, Amr Helal, Mariana Herrera Cruz, Ruben Herreros Ruiz-Valdepeñas, James Horton, Sean Howells, Alan Howieson, Luke Hughes, Flavia Lorena Hünicken Torrez, Ana Hurtado Ortega, Peter Huxley, Hytham K.S. Hamid, Nida Ilahi, Alexis Iliadis, Dominic Inman, Piyush Jadhao, Rajan Jandoo, Lucy Jawad, Malwattage Lara Tania Jayatilaka, Paul J. Jenkins, Rathan Jeyapalan, David Johnson, Andrew Johnston, Sarah Joseph, Siddhant Kapoor, Georgios Karagiannidis, Krishna Saga Karanam, Freddy Kattakayam, Alastair Konarski, Georgios Kontakis, Gregorio Labrador Hernández, Victoria Lancaster, Giovanni Landi, Brian Le, Ignatius Liew, Kartik Logishetty, Andrew Carlomaria Daniel Lopez Marquez, Judit Lopez, Joann Lum, Gavin J. Macpherson, Suvira Madan, Sabreena Mahroof, Khalid Malik-Tabassum, Ravi Mallina, Afnan Maqsood, Ben Marson, M. José Martin Legorburo, Encarna Martin-Perez, Tania Martínez Jiménez, Javier Martinez Martin, Alistair Mayne, Amy Mayor, Gavan McAlinden, Lucille McLean, Lorna McDonald, Joshua McIntyre, Pamela McKay, Greg McKean, Heather McShane, Antonio Medici, Chelsea Meeke, Evonne Meldrum, Mijail Mendez, Scott Mercer, Josu Merino Perez, María-Pilar Mesa-Lampré, Shuna Mighton, Kirsty Milne, Muhammed Mohamed Yaseen, Iain Moppett, Jesus Mora, Sira Morales-Zumel, Irene Blanca Moreno Fenoll, Adham Mousa, Alastair W. Murray, Elspeth V. Murray, Radhika Nair, Fiona Neary, Giacomo Negri, Oliver Negus, Fiona Newham-Harvey, Nigel Ng, Jess Nightingale, Sumiya Noor Mohamed Anver, Perrico Nunag, Matthew O'Hare, Ben Ollivere, Raquel Ortés Gómez, AnneMarie Owens, Siobhan Page, Valentina Palloni, Andreas Panagiotopoulos, Elias Panagiotopoulos, Paul Panesar, Antonios Papadopoulos, Papagiannis Spyridon, Teresa Pareja Sierra, Chang Park, Hammad Parwaiz, Paul Paterson-Byrne, Sam Patton, Jack Pearce, Marina Porter, Achille Pellegrino, Arturo Pèrez Cuellar, Raffaele Pezzella, Ashish Phadnis, Charlotte Pinder, Danielle Piper, Matilda Powell-Bowns, Rocío Prieto Martín, Annabel Probert, Ashwanth Ramesh, Manuel Vicente Mejía Ramírez de Arellano, Duncan Renton, Stephen Rickman, Alastair Robertson, Adrian Roche Albero, José Alberto Rodrigo Verguizas, Myriam Rodríguez Couso, Joanna Rooney, Pilar Sáez-López, Andres Saldaña-Díaz, Adriano Santulli, Marta Isabel Sanz Pérez, Khaled M. Sarraf, Christine Scarsbrook, Chloe E.H. Scott, Jennifer Scott, Sachi Shah, Sharief Sharaf, Sidharth Sharma, Denise Shirley, Antonio Siano, James Simpson, Abhinav Singh, Amit Singh, Tim Sinnett, Gurudatt Sisodia, Philomena Smith, Eugenia Sophena Bert, Michael Steel, Avril Stewart, Claire Stewart, Kapil Sugand, Niall Sullivan, Lauren Sweeting, Michael Symes, Dylan Jun Hao Tan, Francesco Tancredi, Irini Tatani, Philip Thomas, Fraser Thomson, Niamh S. Toner, Anna Tong, Antonio Toro, Theodoros Tosounidis, Stylianos Tottas, Andrea Trinidad Leo, Damien Tucker, Krishna Vemulapalli, Diego Ventura Garces, Olivia Katherine Vernon, Juan Carlos Viveros Garcia, Alex Ward, Kirsty Ward, Kate Watson, Thisara Weerasuriya, Udara Wickramanayake, Hannah Wilkinson, Joseph Windley, Janet Wood, William Wynell-Mayow, Giovanni Zatti, Moez Zeiton, and Miriam Zurrón Lobato
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Surgery - Published
- 2022
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7. Artists Shaping Policies Through Higher Art Education. How Visual Artists Develop Policies that Affect their Lives, Practices, and Careers
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Sarah Scarsbrook
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General Earth and Planetary Sciences ,General Environmental Science - Abstract
This paper centralises visual artists in policymaking processes. It foregrounds the ways artists influence and determine the policies that affect their lives, practices, and careers through their higher art education in London (UK) art schools between 1986-2016. The uninvited and indirect processes by which artists are shaping policies using their education is captured through artsbased/informed methods developed for listening, analysing, and interpreting alongside grounded theory methodology. The practitionerled approach is key to noticing and raising the subtle agitations in the actions and inactions that underscore artists’ role as policy progenitors. Artists’ relationships with professional development and their experiences of structureless pedagogies, which are aligned to artistic myth are foregrounded. Their acceptances, rejections, and reframing of their fine art curricula is where their influence in shaping policy sits.
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- 2022
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8. Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal
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Lachie Scarsbrook, Kieren J. Mitchell, Matthew D. McGee, Gerard P. Closs, and Nicolas J. Rawlence
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Animal Science and Zoology ,Biodiversity ,Ecology, Evolution, Behavior and Systematics ,Taxonomy - Abstract
The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand—including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling—is poorly understood. The New Zealand grayling (Prototroctes oxyrhynchus) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis.Here, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes of P. oxyrhynchus, and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa.We recovered strong evidence for a sister relationship between the New Zealand and Australian grayling (P. mareana), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1–23.2 Mya), after the height of Oligocene marine inundation in New Zealand.Our temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance.This study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA.
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- 2022
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9. Annual Congress of the European Association of Nuclear Medicine October 15-19, 2022 Barcelona, Spain
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Stephen Ahenkorah, Dr. Ashish Kumar Jha, Matthijs Sevenois, ELIF TUGCE SARCAN BOZKIR, Jenni Virta, Alexandra-Maria Lazar, Andrew Scarsbrook, Sneha Mithun, Zbigniew Adamczewski, Heidi Liljenbäck, Dimitri Brigide de Almeida Mantovani, Juhani Knuuti, Thibault Escobar, Lars Poulsen Tolbod, Johanna Marcela Espejo Niño, and Matthias D'Huyvetter
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Radiology, Nuclear Medicine and imaging ,General Medicine - Published
- 2022
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10. Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone
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Kerry Walton, Lachie Scarsbrook, Kieren J. Mitchell, Alexander J. F. Verry, Bruce A. Marshall, Nicolas J. Rawlence, and Hamish G. Spencer
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Phylogeography ,Mollusca ,Gastropoda ,Genetics ,Animals ,DNA ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,New Zealand ,Biotechnology - Abstract
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.
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- 2022
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11. Prediction of prostate tumour hypoxia using pre-treatment MRI-derived radiomics: preliminary findings
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Jim Zhong, Russell Frood, Alan McWilliam, Angela Davey, Jane Shortall, Martin Swinton, Oliver Hulson, Catharine M. West, David Buckley, Sarah Brown, Ananya Choudhury, Peter Hoskin, Ann Henry, and Andrew Scarsbrook
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Radiology, Nuclear Medicine and imaging ,General Medicine - Abstract
Purpose To develop a machine learning (ML) model based on radiomic features (RF) extracted from whole prostate gland magnetic resonance imaging (MRI) for prediction of tumour hypoxia pre-radiotherapy. Material and methods Consecutive patients with high-grade prostate cancer and pre-treatment MRI treated with radiotherapy between 01/12/2007 and 1/08/2013 at two cancer centres were included. Cancers were dichotomised as normoxic or hypoxic using a biopsy-based 32-gene hypoxia signature (Ragnum signature). Prostate segmentation was performed on axial T2-weighted (T2w) sequences using RayStation (v9.1). Histogram standardisation was applied prior to RF extraction. PyRadiomics (v3.0.1) was used to extract RFs for analysis. The cohort was split 80:20 into training and test sets. Six different ML classifiers for distinguishing hypoxia were trained and tuned using five different feature selection models and fivefold cross-validation with 20 repeats. The model with the highest mean validation area under the curve (AUC) receiver operating characteristic (ROC) curve was tested on the unseen set, and AUCs were compared via DeLong test with 95% confidence interval (CI). Results 195 patients were included with 97 (49.7%) having hypoxic tumours. The hypoxia prediction model with best performance was derived using ridge regression and had a test AUC of 0.69 (95% CI: 0.14). The test AUC for the clinical-only model was lower (0.57), but this was not statistically significant (p = 0.35). The five selected RFs included textural and wavelet-transformed features. Conclusion Whole prostate MRI-radiomics has the potential to non-invasively predict tumour hypoxia prior to radiotherapy which may be helpful for individualised treatment optimisation.
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- 2023
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12. UK Lung cancer screening guidelines; are functional adrenal lesions being missed?
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Rebecca Sagar, Andrew Scarsbrook, Matthew Callister, and Afroze Abbas
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General Medicine - Published
- 2023
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13. Multimodality imaging in primary hyperparathyroidism
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A, Zarei, S, Karthik, F U, Chowdhury, C N, Patel, A F, Scarsbrook, and S, Vaidyanathan
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Parathyroid Glands ,Technetium Tc 99m Sestamibi ,Tomography, Emission-Computed, Single-Photon ,Parathyroid Neoplasms ,Humans ,Radiology, Nuclear Medicine and imaging ,General Medicine ,Radiopharmaceuticals ,Hyperparathyroidism, Primary ,Multimodal Imaging - Abstract
Institutional variations in parathyroid adenoma localisation are largely dictated by local experience and availability of imaging investigations, with no consensus on the optimal approach. This review evaluates the role of multiple imaging techniques in primary hyperparathyroidism and highlights their advantages and limitations in different clinical contexts. A clinico-radiological review of parathyroid imaging techniques is illustrated with example cases and data from the literature. These include high-resolution ultrasound
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- 2022
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14. Harmonisation of scanner-dependent contrast variations in magnetic resonance imaging for radiation oncology, using style-blind auto-encoders
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Kavi Fatania, Anna Clark, Russell Frood, Andrew Scarsbrook, Bashar Al-Qaisieh, Stuart Currie, and Michael Nix
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Radiation ,Radiology, Nuclear Medicine and imaging - Abstract
Background and purpose Magnetic Resonance Imaging (MRI) exhibits scanner dependent contrast, which limits generalisability of radiomics and machine-learning for radiation oncology. Current deep-learning harmonisation requires paired data, retraining for new scanners and often suffers from geometry-shift which alters anatomical information. The aim of this study was to investigate style-blind auto-encoders for MRI harmonisation to accommodate unpaired training data, avoid geometry-shift and harmonise data from previously unseen scanners. Materials and methods A style-blind auto-encoder, using adversarial classification on the latent-space, was designed for MRI harmonisation. The public CC359 T1-w MRI brain dataset includes six scanners (three manufacturers, two field strengths), of which five were used for training. MRI from all six (including one unseen) scanner were harmonised to common contrast. Harmonisation extent was quantified via Kolmogorov-Smirnov testing of residual scanner dependence of 3D radiomic features, and compared to WhiteStripe normalisation. Anatomical content preservation was measured through change in structural similarity index on contrast-cycling (δSSIM). Results The percentage of radiomics features showing statistically significant scanner-dependence was reduced from 41% (WhiteStripe) to 16% for white matter and from 39% to 27% for grey matter. δSSIM < 0.0025 on harmonisation and de-harmonisation indicated excellent anatomical content preservation. Conclusions Our method harmonised MRI contrast effectively, preserved critical anatomical details at high fidelity, trained on unpaired data and allowed zero-shot harmonisation. Robust and clinically translatable harmonisation of MRI will enable generalisable radiomic and deep-learning models for a range of applications, including radiation oncology treatment stratification, planning and response monitoring.
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- 2022
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15. Rapid radiation of Southern Ocean shags in response to receding sea ice
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Nicolas J. Rawlence, Alexander T. Salis, Hamish G. Spencer, Jonathan M. Waters, Lachie Scarsbrook, Kieren J. Mitchell, Richard A. Phillips, Luciano Calderón, Timothée R. Cook, Charles‐André Bost, Ludovic Dutoit, Tania M. King, Juan F. Masello, Lisa J. Nupen, Petra Quillfeldt, Norman Ratcliffe, Peter G. Ryan, Charlotte E. Till, and Martyn Kennedy
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Ecology ,sense organs ,Ecology, Evolution, Behavior and Systematics - Abstract
Understanding how natural populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. Blue-eyed shags represent a paradoxical seabird radiation—a circumpolar distribution implies strong dispersal capacity yet their species-rich nature suggests local adaptation and isolation. Here we attempt to resolve this paradox in light of the history of repeated cycles of climate change in the Southern Ocean.
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- 2022
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16. Combined PET-CT and MRI for response evaluation in patients with squamous cell anal carcinoma treated with curative-intent chemoradiotherapy
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Pratik Adusumilli, Noha Elsayed, Stelios Theophanous, Robert Samuel, Rachel Cooper, Nathalie Casanova, Damien J. Tolan, Alexandra Gilbert, and Andrew F. Scarsbrook
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Male ,Epithelial Cells ,Chemoradiotherapy ,General Medicine ,Anus Neoplasms ,Magnetic Resonance Imaging ,Fluorodeoxyglucose F18 ,Positron Emission Tomography Computed Tomography ,Positron-Emission Tomography ,Carcinoma, Squamous Cell ,Humans ,Female ,Radiology, Nuclear Medicine and imaging ,Radiopharmaceuticals ,Retrospective Studies - Abstract
Objectives To assess the effectiveness of fluorine-18 fluorodeoxyglucose (FDG) positron-emission tomography-computed tomography (PET-CT) and magnetic resonance imaging (MRI) for response assessment post curative-intent chemoradiotherapy (CRT) in anal squamous cell carcinoma (ASCC). Methods Consecutive ASCC patients treated with curative-intent CRT at a single centre between January 2018 and April 2020 were retrospectively identified. Clinical meta-data including progression-free survival (PFS) and overall survival (OS) outcomes were collated. Three radiologists evaluated PET-CT and MRI using qualitative response assessment criteria and agreed in consensus. Two-proportion z test was used to compare diagnostic performance metrics (sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy). Kaplan-Meier analysis (Mantel-Cox log-rank) was performed. Results MRI (accuracy 76%, PPV 44.8%, NPV 95.7%) and PET-CT (accuracy 69.3%, PPV 36.7%, NPV 91.1%) performance metrics were similar; when combined, there were statistically significant improvements (accuracy 94.7%, PPV 78.9%, NPV 100%). Kaplan-Meier analysis demonstrated significant differences in PFS between responders and non-responders at PET-CT (p = 0.007), MRI (p = 0.005), and consensus evaluation (p < 0.001). Cox regression analysis of PFS demonstrated a lower hazard ratio (HR) and narrower 95% confidence intervals for consensus findings (HR = 0.093, p < 0.001). Seventy-five patients, of which 52 (69.3%) were females, with median follow-up of 17.8 months (range 5–32.6) were included. Fifteen of the 75 (20%) had persistent anorectal and/or nodal disease after CRT. Three patients died, median time to death 6.2 months (range 5–18.3). Conclusion Combined PET-CT and MRI response assessment post-CRT better predicts subsequent outcome than either modality alone. This could have valuable clinical benefits by guiding personalised risk-adapted patient follow-up. Key Points • MRI and PET-CT performance metrics for assessing response following chemoradiotherapy (CRT) in patients with anal squamous cell carcinoma (ASCC) were similar. • Combined MRI and PET-CT treatment response assessment 3 months after CRT in patients with ASCC was demonstrated to be superior to either modality alone. • A combined MRI and PET-CT assessment 3 months after CRT in patients with ASCC has the potential to improve accuracy and guide optimal patient management with a greater ability to predict outcome than either modality alone
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- 2022
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17. Deep learning with visual explanation for radiotherapy-induced toxicity prediction
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Behnaz Elhaminia, Alexandra Gilbert, Alex Frangi, Andrew Scarsbrook, John Lilley, Ane Allept, Ali Gooya, and Nishant Ravikumar
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- 2023
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18. Impact of 18F-fluciclovine PET/CT on plans for androgen deprivation therapy in patients with biochemical recurrence of prostate cancer: data analysis from two prospective clinical trials
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Gerald L. Andriole, Andrew F. Scarsbrook, and Bital Savir-Baruch
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Oncology ,Urology - Published
- 2023
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19. Hoplodactylus tohu Scarsbrook & Walton & Rawlence & Hitchmough 2023, n. sp
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Scarsbrook, Lachie, Walton, Kerry, Rawlence, Nicolas J., and Hitchmough, Rodney A.
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Hoplodactylus ,Reptilia ,Diplodactylidae ,Hoplodactylus tohu ,Squamata ,Animalia ,Biodiversity ,Chordata ,Gymnophthalmidae ,Taxonomy - Abstract
Hoplodactylus tohu n. sp. Figures 2A, 3A–D, 4A–C; Supplementary Figures 5A–C. ZooBank registration of Hoplodactylus tohu n. sp.: urn:lsid:zoobank.org:pub: BC2A430C-D97C-4F45-9AFB-228379864926. Naultinus pacificus.– Gray 1843: 203 (in part, not Gray, 1842). Hoplodactylus duvaucelii [sic] McCann 1955: 39, fig. 3, pl. 4; McCann 1956a: 46; McCann 1956b: 15; Bustard 1963: 218; Sharell 1966: 49, pls. 28–31; Thoresen 1967: 197; Whitaker 1973: 122; Domrow et al. 1980: 295; Barwick 1982: 377; Bauer 1985: 90; Halliday & Verrell 1988: 260; Wilson & Freeman 1993: 1 – all in part (not Duméril & Bibron, 1836). Hoplodactylus duvaucelii.– Holder 1960: 302; Kluge 1967a: 25; Kluge 1967b: 1013; Werner et al. 1978: 378;7 Kennedy 1979: 1; Bauer 1986: 9; Worthy 1987b: 416; Bauer 1990: 108; Thompson et al. 1992: 123; Daugherty et al. 1993: 439; Bauer & Henle 1994: 139; Cree 1994: 352 Daugherty et al. 1994: 318; Towns & Daugherty 1994: 327; Worthy & Holdaway 1994: 326; East et al. 1995: 256; Worthy & Holdaway 1995: 350; Worthy & Holdaway 1996: 314; Hitchmough 1997: 1; Worthy 1997: 93; Bauer 1998: 43; Girling et al. 1998: 139, fig. 4; Worthy 1998: 448; Bannock et al. 1999: 102; Lukis 1999: 12; Flannagan 2000: 4; Jones 2000: 1, fig. 2.9; Towns & Ferreira 2001: 219; Towns et al. 2001: 4; Seligmann 2002: 277; Whitaker et al. 2002: 1; Hay et al. 2003: 16; Todd 2003: 17; Seligmann et al. 2003: 130; Holmes 2004: 4; Naish 2004: 18; Hare & Cree 2005: 137; Armstrong & Davidson 2006: 74; Hare et al. 2007: 89; Nielsen 2008: 5; Kelly & Sullivan 2010: 208; Miskelly 2010: 3; Wilson 2010: 6; Frank & Wilson 2011: 16; Nielsen et al. 2011: 17; Bell & Herbert 2012: 8; Str̂ckens et al. 2012: 542; Garcia-Porta & Ord 2013: 2667; Hitchmough et al. 2013: 10; Bell 2014: 8; Romijn et al. 2014: 111; Heath & Whitaker 2015: 751; Mockett 2015: 73; Chapple 2016b: 4; Chapple & Hitchmough 2016: 116; Cree & Hare 2016: 174; Hare et al. 2016: 140; Hare & Cree 2016: 246; Hitchmough et al. 2016a: 9; Hitchmough et al. 2016b: 89; Morgan-Richards et al. 2016: 77, fig. 2; Romijn and Hartley 2016: 196; Towns et al. 2016b: 308; Worthy 2016: 71; Bell and Herbert 2017: 38; Bowers 2017: 64; Knox et al. 2017: 490; Lozito & Tuan 2017: 148, fig. 2 Sion 2017: 131; Stancher et al. 2018: 36; van Winkel et al. 2018: 114, pls. 31, 40, 46, 128; Skipwith et al. 2019: 10; Florence-Bennett 2020: 13; Glynne et al. 2020: 804; Herbert 2020: 12; Price et al. 2020: 231; Scarsbrook 2021: 19, figs. 1.5, 2.1, 3.1, 3.3, 4.1; Scarsbrook et al. 2021: 2; Scarsbrook et al. 2022: 3, fig. 1 – all in part (not Duméril & Bibron, 1836). Naultinus duvaucelii.– Chrapliwy et al. 1961: 6 (in part, not Duméril & Bibron, 1836). Woodworthia duvaucelii.– Jewell 2008: 50 (in part, not Duméril & Bibron, 1836). Type material.— Holotype: New Zealand, Marlborough Sounds, Middle Trios Island, male, Y. M. McCann, February 1950, RE.000503. Paratypes: New Zealand, Marlborough Sounds, Middle Trios Island, 40°50.53′ S, 174°0.00′ E, both male, C. H. Daugherty, 22 November 1988, RE.006685, RE.006686 (tissue clips: FT2047, FT2048 respectively). Material examined.— The type material. Stephens Island (OMVT949). Trios Islands: Middle Trios Island (RE.000505,FT2046); South Trios Island (RE.006687). Sentinel Rock (RE.000948). Chetwode Island (RE.000949). Brothers Islands: North Brother Island (RE.002561, RE.005496, RE.006509, RE.006510, RE.007265, FT277, FT278). Northwest South Island (mainland): Gouland Downs, Holocene fossil (S.38813.2). Canterbury (mainland): Waikari, Holocene fossil (S.33501, S.33703.1, S.33703.7, S.33703.10, S.33703.11); Waitaki, Holocene fossil (OMVT719 a, OMVT807 a, OMVT807 b, OMVT3331, OMVT3332, OMVT3333). Diagnosis.— Hoplodactylus tohu may be distinguished from its only congener, H. duvaucelii, by several characters: H. tohu (generally) does not attain as great a size at maturity (Supp. Fig. 1), has a more pronounced brillar fold (Fig. 3A–B, E–F, 4C, F), and less often bears a median cleft in the mental scale (Supp. Table 3). An abrupt size decrease at the 5 th infralabial scale characterizing H. tohu is far less common in H. duvaucelii, with most individuals of the latter examined exhibiting a gradual size decrease in infralabial scales (Fig. 3B, F). H. tohu further differs from H. duvaucelii in generally having fewer subdigital lamellae on all digits of both the right manus and pes (Fig. 3C–D, G–H, Supp. Fig. 3). The first digit of the right manus in H. duvaucelii differs in having a consistently less emergent claw and, usually, a comparatively bulbous distal end (Fig. 3C, G). Previously reported differences (Morgan-Richards et al. 2016) in the coloration and extent of patterning between these taxa (Fig. 4) are generalizations and can be misleading given fluid overlap between the two species. Dorsal body coloration and patterning in H. tohu often resembles those of young H. duvaucelii in being relatively more strongly contrasting (Fig. 4A–B, D–E), with patterning generally becoming weaker at maturity. However, considerable variation in coloration and pattern (see Supp. Fig. 5) was observed throughout ontogeny in both species. Description.— Coloration on dorsal surface grey to grey-brown, sometimes with olive and dark brown blotches; patterning of well-developed, roughly symmetrical transverse bands from nape to tail base centered along spine, resembling chevrons or paired diamonds, less defined on tail and generally less defined on older individuals; often bearing irregular series of longitudinal rows of pale grey or white spots dorsolaterally, extending onto limbs; ventral surface buff, with occasional light brown speckling, speckles less frequent on head. Mouth lining and tongue pink. Body moderately large (SVL: 81.2–115.7 mm), robust, stout (TrK: 25.4–50.3 mm). Head large (HL: 26.1–33.8 mm; HW: 18.3–27 mm; HH: 12.2–16 mm), robust, subtriangular; inflated laterally between posterior edge of orbit and ear opening (EE: 7.7–11.8 mm), narrowing towards craniovertebral junction; neck clearly demarcated. Snout oviform (EN: 7.4–11.1 mm); slight indentation in medial nasal region, often blunt along anteriormost margin between nares (IN: 4–5.8 mm). Dorsum of occiput/nape covered in small granular scales that abruptly increase in size at level of anterior edge of orbit towards anterior margin of snout (2–3 times diameter of occipital granules); one row of enlarged, oval scales posterior to internasal(s) and dorsal to supralabials, broader than high; twice the diameter of adjacent loreal scales. Eyes approximately one fifth head length; varying in shade from pale olive-buff to dark greens or browns; pupils lenticular with weakly crenulated margin. Supraciliary scales elongate, conical, directed increasingly posterior posteriorly; brillar fold very pronounced; frontal narrowing anteriorly (IO: 7.8–11.8 mm), supraocular portion deeply furrowed. Ear opening moderate (EL: 2–4.1 mm), ovoid, twice as high as wide; oriented obliquely (widest posterodorsally to anteroventrally), skin fold covering dorsal limit. Rostral subpentagonal, much broader than high; contacted dorsally by 2 enlarged, oval supranasals and 1–3 smaller (homogenous), round internasals; medial rostral crease extending ventrally from upper margin ½ to ¾ length of rostral; usually terminating diffusely, but sometimes as an ovoid crease. Nares rounded, situated anterolaterally; bordered by rostral, supranasal, 3–5 small postnasals and first supralabial. Supralabials rectangular, rounded dorsally; slightly higher than broad; numbering 13–16 per side; gradually decreasing in size posteriorly; final 3–4 more narrowly convex; supralabials terminating beneath the posterior orbital margin (with 11 or 12 beneath orbit midline); posteriormost twice the size of loreal scales. Mental trapezoidal to subtriangular, with longest face along jaw margin, narrowing posteriorly; mental crease usually absent, extending ½ length of scale where present; mental shorter than laterally adjacent first infralabials; contacted posteriorly by 1 large or 2 smaller hexagonal postmentals, which separate infralabials. Infralabials numbering 9–14 per side; from the snout, infralabials 1–4 on each side are quadrate, more rounded ventrally, higher than broad; infralabial 5 usually marks commencement of a significant and discrete infralabial size decrease, sometimes on one side only, with subsequent infralabials becoming progressively smaller and increasingly circular in shape, terminating in-line with the posterior orbital margin. Anterior infralabials and postmental(s) bordered posteriorly by series of enlarged irregular chin shields; rows indistinct; anteriormost approximately ¾ diameter of postmental, with gradual transition to very small, rounded throat granules posteriorly. Dorsal scales small, mostly homogenous in size, bead-like, apically flattened, partially overlain; indistinct from scales of nape. Ventral scales roughly twice diameter of dorsal scales, circular, flattened, subimbricate, slightly enlarged in precloacal region, extending in rows onto thighs where they form a subtriangular patch; transition to granules at throat abrupt. Skin folds extending ventrolaterally along trunk; anteroposterior folds above fore- and hindlimb insertion. Limbs relatively short and robust, hindlimbs longer; scales on forelimb dorsum larger than dorsal body scales, subimbricate distally; ventral forelimb scales smaller than those dorsally; clear transition to enlarged scales of palm which resemble ventral body scales. Scales on preaxial surface of thigh enlarged, up to three times diameter of dorsal body scales at knee; circular, subimbricate; gradually decreasing in size both posteriorly and distally (along shin) to smaller granules; transition to scales of soles indistinct (resembling ventral body scales). 5–6 rows of precloacal pores in males, anteriormost 2 rows extending distally just over halfway along hind thigh; absent in females. Digits broad, with dilated pads on digits II–V that rapidly transition into slender distal extension, mostly of constant width but becoming narrowly tapered near distal end; digit I smallest on all feet, digit IV longest on manus, digit V longest on pes; angle at rest between digits IV and V greatest, greater on pes than manus; digits II–V of pes and I–IV of manus very weakly webbed; dorsal scales on digits large, especially on first digit; all digits bear recurved, mostly exposed claws. Basalmost 1–2 subdigital lamellae sometimes fragmented; unfragmented subdigital lamellae curved outwards, usually smoothly but sometimes more sharply curved medially; lamellar counts of right manus: 6–7 (I), 9–11 (II), 12–14 (III), 12–15 (IV), 9–11 (V), and pes: 6–9 (I), 10–13 (II), 14–16 (III), 14–18 (IV), 11–16 (V) digits. Tail (original) stout, shorter than SVL, gradually tapered to end, roughly circular in cross-section; often lost through autotomy and then regenerated. Regenerated tail demarcated by abrupt decrease in scale size and anteroposterior striations from point of detachment distally. Base of tail distinctly swollen (TW: 8.7–14.7), most notable in males at cloacal spurs, with enlarged hexagonal scales on underside roughly twice size of more anterior ventral scales. Caudal scales usually arranged in discrete, irregular rows, generally decreasing in size distally from the septum; autotomy septa visibly marked by one, sometimes two rows of large or smaller scales, separated by 9–11 scale rows; dorsal caudal scales approximately 1.5 times size of dorsal body scales, demarcating tail base; highly variable in both size and shape, circular to rounded rectangular; ventral caudal scales enlarged medially, twice as large as dorsal; rectangular to hexagonal, higher than broad, subimbricate. Cloacal spurs consisting of a set of greatly enlarged, conical scales, with most acute point orientated posterodorsally, situated adjacent to cloaca (laterally); often asymmetric in number: 2–5 (L) and 1–4 (R), first (largest) roughly twice size of ventral scales, decreasing in size posteriorly. Distribution.— New Zealand: formerly throughout the South Island (Holocene); presently restricted to some islands in the outer Marlborough Sounds and Cook Strait (Fig. 1). Remarks.— Hoplodactylus tohu has been recognized as distinct from H. duvaucelii for several years (MorganRichards et al. 2016; Hitchmough et al. 2021a). However, it has been unclear what rank to apply to this taxon. New Zealand diplodactylids frequently have highly conserved morphologies, and often greater intra- than inter-specific morphological variation (Hitchmough et al. 2016b). With both Hoplodactylus species recognized here having undergone recent major range contractions resulting in significant declines in morphological and genetic diversity (Scarsbrook et al. 2021; Scarsbrook et al. 2022), it is difficult to weight subtle character differences as these may have arisen, or increased in prevalence, recently, through chance, in relictual populations, and therefore not reflect deeper evolutionary divergences. That these taxa have been reported to produce viable cross-bred offspring in captive populations (Morgan-Richards et al. 2016) fails to meet the criteria of the Biological Species Concept (Mayr 1942). Reproductive isolation in the wild cannot be tested given their allopatric distributions. However, several pairings of lizard species that are widely recognized to be distinct (Brennan et al. 2016; Leaché & Cole 2006; Olave et al. 2011), including some other New Zealand diplodactylids (e.g., Naultinus sp.; Hitchmough et al. 2016b), have been shown to similarly produce viable hybrid offspring. Intergeneric hybrids have even been reported (RH pers. obs). Genetic distance (i.e., ~2.2% and ~4.0% across the mitochondrial genome and ND2 respectively) and estimated timing of lineage divergence of ~4.51 mya (Scarsbrook et al. 2022) between the two Hoplodactylus species recognized here are comparable with those of other recognized diplodactylid species pairings (e.g., 3.8% ND2 divergence between Mokopirirakau kahutarae Whitaker, 1985, and Mokopirirakau granulatus Gray, 1845; Knox et al. 2021). Their discrete (allopatric) distributions reflect commonly observed biogeographic patterns in other taxa (Baker et al. 1995; Efford et al. 2002; Greaves et al. 2007; Liggins et al. 2008; Lloyd 2003), which further influences our treatment of species-level distinction. Reports of interbreeding between H. tohu and H. duvaucelii in captivity makes careful management of both species essential to maintain species/genetic integrity. Individuals sourced for reintroduction or translocation purposes need to be of the correct species, and sourced from moderately large and stable populations (e.g. North Brother Island; Wilson 2010) to minimise impact on the source population. Further, source populations should be proximate (where practicable) to the site of translocation to ensure preservation of regional adaptations; a consideration more applicable to H. duvaucelii as extant populations are more numerous and occupy more ecologically varied habitats. It seems probable, for example, that H. duvaucelii rather than H. tohu, would have naturally occurred at Mana Island, off the southern North Island. However, the latter was translocated there from North Brother Island in 1998 through the release of 40 individuals (Miskelly 2010), with a self-sustaining population reported 15-years later (Bell & Herbert 2017). H. tohu has been recognized as a distinct management unit by the Department of Conservation since 2021 (Hitchmough et al. 2021a), listed as “nationally increasing” with the ‘Conservation Dependant’ and ‘Range Restricted’ qualifiers. H. tohu has a severely restricted distribution comprising a few islands (Fig. 1; Supp. Table 1) with highly anthropogenically modified habitats. The estimated total population size of the largest extant population, on the Brothers Islands, is between 583–677 (Wilson 2010). Based on this, the suggested IUCN Red List status of H. tohu is ‘Critically Endangered A1 (a, b, c, e)’: population reduction of>90% observed, estimated, inferred, or suspected in the past where the causes of the reduction are clearly reversible AND understood AND have ceased. Occurrence of H. tohu on several managed predator-free islands that already have conservation management strategies in place does at least render moderate security to this species from localized disturbances such as fire or predator incursions. However, additional protection through translocations to fenced and more distant mainland sanctuaries (e.g. Orokonui Ecosanctuary near Dunedin, and the Mokomoko Dryland Sanctuary in Central Otago) could be beneficial, given the increased vulnerability of small and sparsely forested islands to the effects of climate change (e.g. sea-level rise, coastal erosion, storm intensity; Macinnis-Ng et al. 2021). Such translocation may also facilitate the re-establishment of ‘lost’ ecological interactions and morphological diversity (e.g. Scarsbrook et al. 2021) specific to mainland and densely forested ecosystems. There is evidence of genetic sub-structuring (Scarsbrook et al. 2022) within the distribution of H. tohu, although this has been greatly reduced with the extinction of mainland South Island populations. Careful management, and possible further research should consider if individual populations are experiencing inbreeding depression and might benefit from genetic rescue – establishment of ‘new’ populations through interbreeding of individuals from different populations to increase genetic ‘fitness’ (i.e., adaptability). Conversely, continued maintenance of discrete lineages may also be appropriate if those lineages reflect local habitat adaptations or if pooled populations would comprise too few individuals to maintain the resulting genetic diversity due to genetic drift. Etymology.— The specific epithet was proposed by Dr Sharon Barcello-Gemmel, Rangatira of Te Ātiawa o Te Waka-a-Māui Trust, in recognition of the tupuna [ancestor] Tohu Kākahi. Tohu Kākahi was one of the two Parihaka prophets with whakapapa [genealogical] connections to Te Ātiawa – the iwi [tribe] with mana whenua [authority] over Ngāwhatu Kai Ponu [The Brothers], where the largest extant population occurs. Name used as noun in apposition.
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20. Freshwater science–policy interactions in Aotearoa-New Zealand: lessons from the past and recommendations for the future
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Scott T. Larned, Clive Howard-Williams, Ken Taylor, and Mike Scarsbrook
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Water Science and Technology - Published
- 2022
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21. Protocol for a MULTI-centre feasibility study to assess the use of 99mTc-sestaMIBI SPECT/CT in the diagnosis of kidney tumours (MULTI-MIBI study)
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Warren, Hannah, Wagner, Thomas, Gorin, Michael A, Rowe, Steven, Holman, Beverley Fiona, Pencharz, Deborah, El-Sheikh, Soha, Barod, Ravi, Patki, Prasad, Mumtaz, Faiz, Bex, Axel, Kasivisvanathan, Veeru, Moore, Caroline M, Campain, Nicholas, Cartledge, Jon, Scarsbrook, Andrew, Hassan, Fahim, O'Brien, Tim S, Stewart, Grant D, Mendichovszky, Iosif, Dizdarevic, Sabina, Alanbuki, Ammar, Wildgoose, William H, Wah, Tze, Vindrola-Padros, Cecilia, Pizzo, Elena, Dehbi, Hakim-Moulay, Lorgelly, Paula, Gurusamy, Kurinchi, Emberton, Mark, Tran, Maxine GB, Warren, Hannah [0000-0002-4106-2705], Kasivisvanathan, Veeru [0000-0002-0832-382X], Moore, Caroline M [0000-0003-0202-7912], Stewart, Grant D [0000-0003-3188-9140], Vindrola-Padros, Cecilia [0000-0001-7859-1646], Gurusamy, Kurinchi [0000-0002-0313-9134], Emberton, Mark [0000-0003-4230-0338], and Apollo - University of Cambridge Repository
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Technetium Tc 99m Sestamibi ,Tomography, Emission-Computed, Single-Photon ,Urology ,Urological tumours ,HEALTH ECONOMICS ,Kidney Neoplasms ,Nuclear radiology ,Humans ,Feasibility Studies ,Multicenter Studies as Topic ,Prospective Studies ,Radiopharmaceuticals ,Tomography, X-Ray Computed - Abstract
Peer reviewed: True, Acknowledgements: We are grateful for the invaluable contribution provided by patient representatives. HW is funded by The Urology Foundation and Pan London Cancer Alliance (Royal Marsden Partners, North Central London Cancer Alliance, North East London Cancer Alliance, South East London Cancer Alliance and the NIHR BRCs). VK receives funding from Prostate Cancer UK and the John Black Charitable Foundation. GDS and IAM are supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014) and GDS by the Cancer Research UK Cambridge Centre [C9685/A25177]. EP is supported by the NIHR Collaboration for Leadership in Applied Health Research and Care (CLAHRC) North Thames at Bart’s Health NHS Trust. Mark Emberton receives research support from the United Kingdom’s National Institute of Health Research (NIHR) UCLH / UCL Biomedical Research Centre. He was conferred NIHR Senior Investigator Status in 2015. MGBT receives research funding from NIHR, St Peter’s Trust, Royal Free Charity, RCS, Facing up 2 Kidney Cancer and Kidney Cancer UK. The views expressed are those of the authors and not necessarily those of the funders., INTRODUCTION: The incidence of renal tumours is increasing and anatomic imaging cannot reliably distinguish benign tumours from renal cell carcinoma. Up to 30% of renal tumours are benign, with oncocytomas the most common type. Biopsy has not been routinely adopted in many centres due to concerns surrounding non-diagnostic rate, bleeding and tumour seeding. As a result, benign masses are often unnecessarily surgically resected. 99mTc-sestamibi SPECT/CT has shown high diagnostic accuracy for benign renal oncocytomas and other oncocytic renal neoplasms of low malignant potential in single-centre studies. The primary aim of MULTI-MIBI is to assess feasibility of a multicentre study of 99mTc-sestamibi SPECT/CT against a reference standard of histopathology from surgical resection or biopsy. Secondary aims of the study include obtaining estimates of 99mTc-sestamibi SPECT/CT sensitivity and specificity and to inform the design and conduct of a future definitive trial. METHODS AND ANALYSIS: A feasibility prospective multicentre study of participants with indeterminate, clinical T1 renal tumours to undergo 99mTc-sestamibi SPECT/CT (index test) compared with histopathology from biopsy or surgical resection (reference test). Interpretation of the index and reference tests will be blinded to the results of the other. Recruitment rate as well as estimates of sensitivity, specificity, positive and negative predictive value will be reported. Semistructured interviews with patients and clinicians will provide qualitative data to inform onward trial design and delivery. Training materials for 99mTc-sestamibi SPECT/CT interpretation will be developed, assessed and optimised. Early health economic modelling using a decision analytic approach for different diagnostic strategies will be performed to understand the potential cost-effectiveness of 99mTc-sestamibi SPECT/CT. ETHICS AND DISSEMINATION: Ethical approval has been granted (UK HRA REC 20/YH/0279) protocol V.5.0 dated 21/6/2022. Study outputs will be presented and published nationally and internationally. TRIAL REGISTRATION NUMBER: ISRCTN12572202.
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22. Revision of the New Zealand gecko genus Hoplodactylus, with the description of a new species
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LACHIE SCARSBROOK, KERRY WALTON, NICOLAS J. RAWLENCE, and RODNEY A. HITCHMOUGH
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Reptilia ,Diplodactylidae ,Squamata ,Animalia ,Animal Science and Zoology ,Biodiversity ,Chordata ,Ecology, Evolution, Behavior and Systematics ,Taxonomy - Abstract
The New Zealand endemic gecko genus Hoplodactylus is revised. Two species are recognized: Hoplodactylus duvaucelii (Duméril & Bibron, 1836) from the North Island and some near-shore islands, and H. tohu n. sp., which was formerly widespread throughout the South Island but is presently restricted to some islands in the Cook Strait region. H. delcourti (Bauer & Russell, 1986) is retained in Hoplodactylus sensu lato in the interest of taxonomic stability, pending further research, but is probably neither congeneric nor from New Zealand.
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23. Hoplodactylus tohu Scarsbrook & Walton & Rawlence & Hitchmough 2023, n. sp
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Scarsbrook, Lachie, Walton, Kerry, Rawlence, Nicolas J., and Hitchmough, Rodney A.
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Hoplodactylus ,Reptilia ,Diplodactylidae ,Hoplodactylus tohu ,Squamata ,Animalia ,Biodiversity ,Chordata ,Taxonomy - Abstract
Hoplodactylus tohu n. sp. Figures 2A, 3A–D, 4A–C; Supplementary Figures 5A–C. ZooBank registration of Hoplodactylus tohu n. sp.: urn:lsid:zoobank.org:pub: BC2A430C-D97C-4F45-9AFB-228379864926. Naultinus pacificus.– Gray 1843: 203 (in part, not Gray, 1842). Hoplodactylus duvaucelii [sic] McCann 1955: 39, fig. 3, pl. 4; McCann 1956a: 46; McCann 1956b: 15; Bustard 1963: 218; Sharell 1966: 49, pls. 28–31; Thoresen 1967: 197; Whitaker 1973: 122; Domrow et al. 1980: 295; Barwick 1982: 377; Bauer 1985: 90; Halliday & Verrell 1988: 260; Wilson & Freeman 1993: 1 – all in part (not Duméril & Bibron, 1836). Hoplodactylus duvaucelii.– Holder 1960: 302; Kluge 1967a: 25; Kluge 1967b: 1013; Werner et al. 1978: 378;7 Kennedy 1979: 1; Bauer 1986: 9; Worthy 1987b: 416; Bauer 1990: 108; Thompson et al. 1992: 123; Daugherty et al. 1993: 439; Bauer & Henle 1994: 139; Cree 1994: 352 Daugherty et al. 1994: 318; Towns & Daugherty 1994: 327; Worthy & Holdaway 1994: 326; East et al. 1995: 256; Worthy & Holdaway 1995: 350; Worthy & Holdaway 1996: 314; Hitchmough 1997: 1; Worthy 1997: 93; Bauer 1998: 43; Girling et al. 1998: 139, fig. 4; Worthy 1998: 448; Bannock et al. 1999: 102; Lukis 1999: 12; Flannagan 2000: 4; Jones 2000: 1, fig. 2.9; Towns & Ferreira 2001: 219; Towns et al. 2001: 4; Seligmann 2002: 277; Whitaker et al. 2002: 1; Hay et al. 2003: 16; Todd 2003: 17; Seligmann et al. 2003: 130; Holmes 2004: 4; Naish 2004: 18; Hare & Cree 2005: 137; Armstrong & Davidson 2006: 74; Hare et al. 2007: 89; Nielsen 2008: 5; Kelly & Sullivan 2010: 208; Miskelly 2010: 3; Wilson 2010: 6; Frank & Wilson 2011: 16; Nielsen et al. 2011: 17; Bell & Herbert 2012: 8; Str̂ckens et al. 2012: 542; Garcia-Porta & Ord 2013: 2667; Hitchmough et al. 2013: 10; Bell 2014: 8; Romijn et al. 2014: 111; Heath & Whitaker 2015: 751; Mockett 2015: 73; Chapple 2016b: 4; Chapple & Hitchmough 2016: 116; Cree & Hare 2016: 174; Hare et al. 2016: 140; Hare & Cree 2016: 246; Hitchmough et al. 2016a: 9; Hitchmough et al. 2016b: 89; Morgan-Richards et al. 2016: 77, fig. 2; Romijn and Hartley 2016: 196; Towns et al. 2016b: 308; Worthy 2016: 71; Bell and Herbert 2017: 38; Bowers 2017: 64; Knox et al. 2017: 490; Lozito & Tuan 2017: 148, fig. 2 Sion 2017: 131; Stancher et al. 2018: 36; van Winkel et al. 2018: 114, pls. 31, 40, 46, 128; Skipwith et al. 2019: 10; Florence-Bennett 2020: 13; Glynne et al. 2020: 804; Herbert 2020: 12; Price et al. 2020: 231; Scarsbrook 2021: 19, figs. 1.5, 2.1, 3.1, 3.3, 4.1; Scarsbrook et al. 2021: 2; Scarsbrook et al. 2022: 3, fig. 1 – all in part (not Duméril & Bibron, 1836). Naultinus duvaucelii.– Chrapliwy et al. 1961: 6 (in part, not Duméril & Bibron, 1836). Woodworthia duvaucelii.– Jewell 2008: 50 (in part, not Duméril & Bibron, 1836). Type material.— Holotype: New Zealand, Marlborough Sounds, Middle Trios Island, male, Y. M. McCann, February 1950, RE.000503. Paratypes: New Zealand, Marlborough Sounds, Middle Trios Island, 40°50.53′ S, 174°0.00′ E, both male, C. H. Daugherty, 22 November 1988, RE.006685, RE.006686 (tissue clips: FT2047, FT2048 respectively). Material examined.— The type material. Stephens Island (OMVT949). Trios Islands: Middle Trios Island (RE.000505,FT2046); South Trios Island (RE.006687). Sentinel Rock (RE.000948). Chetwode Island (RE.000949). Brothers Islands: North Brother Island (RE.002561, RE.005496, RE.006509, RE.006510, RE.007265, FT277, FT278). Northwest South Island (mainland): Gouland Downs, Holocene fossil (S.38813.2). Canterbury (mainland): Waikari, Holocene fossil (S.33501, S.33703.1, S.33703.7, S.33703.10, S.33703.11); Waitaki, Holocene fossil (OMVT719 a, OMVT807 a, OMVT807 b, OMVT3331, OMVT3332, OMVT3333). Diagnosis.— Hoplodactylus tohu may be distinguished from its only congener, H. duvaucelii, by several characters: H. tohu (generally) does not attain as great a size at maturity (Supp. Fig. 1), has a more pronounced brillar fold (Fig. 3A–B, E–F, 4C, F), and less often bears a median cleft in the mental scale (Supp. Table 3). An abrupt size decrease at the 5 th infralabial scale characterizing H. tohu is far less common in H. duvaucelii, with most individuals of the latter examined exhibiting a gradual size decrease in infralabial scales (Fig. 3B, F). H. tohu further differs from H. duvaucelii in generally having fewer subdigital lamellae on all digits of both the right manus and pes (Fig. 3C–D, G–H, Supp. Fig. 3). The first digit of the right manus in H. duvaucelii differs in having a consistently less emergent claw and, usually, a comparatively bulbous distal end (Fig. 3C, G). Previously reported differences (Morgan-Richards et al. 2016) in the coloration and extent of patterning between these taxa (Fig. 4) are generalizations and can be misleading given fluid overlap between the two species. Dorsal body coloration and patterning in H. tohu often resembles those of young H. duvaucelii in being relatively more strongly contrasting (Fig. 4A–B, D–E), with patterning generally becoming weaker at maturity. However, considerable variation in coloration and pattern (see Supp. Fig. 5) was observed throughout ontogeny in both species. Description.— Coloration on dorsal surface grey to grey-brown, sometimes with olive and dark brown blotches; patterning of well-developed, roughly symmetrical transverse bands from nape to tail base centered along spine, resembling chevrons or paired diamonds, less defined on tail and generally less defined on older individuals; often bearing irregular series of longitudinal rows of pale grey or white spots dorsolaterally, extending onto limbs; ventral surface buff, with occasional light brown speckling, speckles less frequent on head. Mouth lining and tongue pink. Body moderately large (SVL: 81.2–115.7 mm), robust, stout (TrK: 25.4–50.3 mm). Head large (HL: 26.1–33.8 mm; HW: 18.3–27 mm; HH: 12.2–16 mm), robust, subtriangular; inflated laterally between posterior edge of orbit and ear opening (EE: 7.7–11.8 mm), narrowing towards craniovertebral junction; neck clearly demarcated. Snout oviform (EN: 7.4–11.1 mm); slight indentation in medial nasal region, often blunt along anteriormost margin between nares (IN: 4–5.8 mm). Dorsum of occiput/nape covered in small granular scales that abruptly increase in size at level of anterior edge of orbit towards anterior margin of snout (2–3 times diameter of occipital granules); one row of enlarged, oval scales posterior to internasal(s) and dorsal to supralabials, broader than high; twice the diameter of adjacent loreal scales. Eyes approximately one fifth head length; varying in shade from pale olive-buff to dark greens or browns; pupils lenticular with weakly crenulated margin. Supraciliary scales elongate, conical, directed increasingly posterior posteriorly; brillar fold very pronounced; frontal narrowing anteriorly (IO: 7.8–11.8 mm), supraocular portion deeply furrowed. Ear opening moderate (EL: 2–4.1 mm), ovoid, twice as high as wide; oriented obliquely (widest posterodorsally to anteroventrally), skin fold covering dorsal limit. Rostral subpentagonal, much broader than high; contacted dorsally by 2 enlarged, oval supranasals and 1–3 smaller (homogenous), round internasals; medial rostral crease extending ventrally from upper margin ½ to ¾ length of rostral; usually terminating diffusely, but sometimes as an ovoid crease. Nares rounded, situated anterolaterally; bordered by rostral, supranasal, 3–5 small postnasals and first supralabial. Supralabials rectangular, rounded dorsally; slightly higher than broad; numbering 13–16 per side; gradually decreasing in size posteriorly; final 3–4 more narrowly convex; supralabials terminating beneath the posterior orbital margin (with 11 or 12 beneath orbit midline); posteriormost twice the size of loreal scales. Mental trapezoidal to subtriangular, with longest face along jaw margin, narrowing posteriorly; mental crease usually absent, extending ½ length of scale where present; mental shorter than laterally adjacent first infralabials; contacted posteriorly by 1 large or 2 smaller hexagonal postmentals, which separate infralabials. Infralabials numbering 9–14 per side; from the snout, infralabials 1–4 on each side are quadrate, more rounded ventrally, higher than broad; infralabial 5 usually marks commencement of a significant and discrete infralabial size decrease, sometimes on one side only, with subsequent infralabials becoming progressively smaller and increasingly circular in shape, terminating in-line with the posterior orbital margin. Anterior infralabials and postmental(s) bordered posteriorly by series of enlarged irregular chin shields; rows indistinct; anteriormost approximately ¾ diameter of postmental, with gradual transition to very small, rounded throat granules posteriorly. Dorsal scales small, mostly homogenous in size, bead-like, apically flattened, partially overlain; indistinct from scales of nape. Ventral scales roughly twice diameter of dorsal scales, circular, flattened, subimbricate, slightly enlarged in precloacal region, extending in rows onto thighs where they form a subtriangular patch; transition to granules at throat abrupt. Skin folds extending ventrolaterally along trunk; anteroposterior folds above fore- and hindlimb insertion. Limbs relatively short and robust, hindlimbs longer; scales on forelimb dorsum larger than dorsal body scales, subimbricate distally; ventral forelimb scales smaller than those dorsally; clear transition to enlarged scales of palm which resemble ventral body scales. Scales on preaxial surface of thigh enlarged, up to three times diameter of dorsal body scales at knee; circular, subimbricate; gradually decreasing in size both posteriorly and distally (along shin) to smaller granules; transition to scales of soles indistinct (resembling ventral body scales). 5–6 rows of precloacal pores in males, anteriormost 2 rows extending distally just over halfway along hind thigh; absent in females. Digits broad, with dilated pads on digits II–V that rapidly transition into slender distal extension, mostly of constant width but becoming narrowly tapered near distal end; digit I smallest on all feet, digit IV longest on manus, digit V longest on pes; angle at rest between digits IV and V greatest, greater on pes than manus; digits II–V of pes and I–IV of manus very weakly webbed; dorsal scales on digits large, especially on first digit; all digits bear recurved, mostly exposed claws. Basalmost 1–2 subdigital lamellae sometimes fragmented; unfragmented subdigital lamellae curved outwards, usually smoothly but sometimes more sharply curved medially; lamellar counts of right manus: 6–7 (I), 9–11 (II), 12–14 (III), 12–15 (IV), 9–11 (V), and pes: 6–9 (I), 10–13 (II), 14–16 (III), 14–18 (IV), 11–16 (V) digits. Tail (original) stout, shorter than SVL, gradually tapered to end, roughly circular in cross-section; often lost through autotomy and then regenerated. Regenerated tail demarcated by abrupt decrease in scale size and anteroposterior striations from point of detachment distally. Base of tail distinctly swollen (TW: 8.7–14.7), most notable in males at cloacal spurs, with enlarged hexagonal scales on underside roughly twice size of more anterior ventral scales. Caudal scales usually arranged in discrete, irregular rows, generally decreasing in size distally from the septum; autotomy septa visibly marked by one, sometimes two rows of large or smaller scales, separated by 9–11 scale rows; dorsal caudal scales approximately 1.5 times size of dorsal body scales, demarcating tail base; highly variable in both size and shape, circular to rounded rectangular; ventral caudal scales enlarged medially, twice as large as dorsal; rectangular to hexagonal, higher than broad, subimbricate. Cloacal spurs consisting of a set of greatly enlarged, conical scales, with most acute point orientated posterodorsally, situated adjacent to cloaca (laterally); often asymmetric in number: 2–5 (L) and 1–4 (R), first (largest) roughly twice size of ventral scales, decreasing in size posteriorly. Distribution.— New Zealand: formerly throughout the South Island (Holocene); presently restricted to some islands in the outer Marlborough Sounds and Cook Strait (Fig. 1). Remarks.— Hoplodactylus tohu has been recognized as distinct from H. duvaucelii for several years (MorganRichards et al. 2016; Hitchmough et al. 2021a). However, it has been unclear what rank to apply to this taxon. New Zealand diplodactylids frequently have highly conserved morphologies, and often greater intra- than inter-specific morphological variation (Hitchmough et al. 2016b). With both Hoplodactylus species recognized here having undergone recent major range contractions resulting in significant declines in morphological and genetic diversity (Scarsbrook et al. 2021; Scarsbrook et al. 2022), it is difficult to weight subtle character differences as these may have arisen, or increased in prevalence, recently, through chance, in relictual populations, and therefore not reflect deeper evolutionary divergences. That these taxa have been reported to produce viable cross-bred offspring in captive populations (Morgan-Richards et al. 2016) fails to meet the criteria of the Biological Species Concept (Mayr 1942). Reproductive isolation in the wild cannot be tested given their allopatric distributions. However, several pairings of lizard species that are widely recognized to be distinct (Brennan et al. 2016; Leaché & Cole 2006; Olave et al. 2011), including some other New Zealand diplodactylids (e.g., Naultinus sp.; Hitchmough et al. 2016b), have been shown to similarly produce viable hybrid offspring. Intergeneric hybrids have even been reported (RH pers. obs). Genetic distance (i.e., ~2.2% and ~4.0% across the mitochondrial genome and ND2 respectively) and estimated timing of lineage divergence of ~4.51 mya (Scarsbrook et al. 2022) between the two Hoplodactylus species recognized here are comparable with those of other recognized diplodactylid species pairings (e.g., 3.8% ND2 divergence between Mokopirirakau kahutarae Whitaker, 1985, and Mokopirirakau granulatus Gray, 1845; Knox et al. 2021). Their discrete (allopatric) distributions reflect commonly observed biogeographic patterns in other taxa (Baker et al. 1995; Efford et al. 2002; Greaves et al. 2007; Liggins et al. 2008; Lloyd 2003), which further influences our treatment of species-level distinction. Reports of interbreeding between H. tohu and H. duvaucelii in captivity makes careful management of both species essential to maintain species/genetic integrity. Individuals sourced for reintroduction or translocation purposes need to be of the correct species, and sourced from moderately large and stable populations (e.g. North Brother Island; Wilson 2010) to minimise impact on the source population. Further, source populations should be proximate (where practicable) to the site of translocation to ensure preservation of regional adaptations; a consideration more applicable to H. duvaucelii as extant populations are more numerous and occupy more ecologically varied habitats. It seems probable, for example, that H. duvaucelii rather than H. tohu, would have naturally occurred at Mana Island, off the southern North Island. However, the latter was translocated there from North Brother Island in 1998 through the release of 40 individuals (Miskelly 2010), with a self-sustaining population reported 15-years later (Bell & Herbert 2017). H. tohu has been recognized as a distinct management unit by the Department of Conservation since 2021 (Hitchmough et al. 2021a), listed as “nationally increasing” with the ‘Conservation Dependant’ and ‘Range Restricted’ qualifiers. H. tohu has a severely restricted distribution comprising a few islands (Fig. 1; Supp. Table 1) with highly anthropogenically modified habitats. The estimated total population size of the largest extant population, on the Brothers Islands, is between 583–677 (Wilson 2010). Based on this, the suggested IUCN Red List status of H. tohu is ‘Critically Endangered A1 (a, b, c, e)’: population reduction of>90% observed, estimated, inferred, or suspected in the past where the causes of the reduction are clearly reversible AND understood AND have ceased. Occurrence of H. tohu on several managed predator-free islands that already have conservation management strategies in place does at least render moderate security to this species from localized disturbances such as fire or predator incursions. However, additional protection through translocations to fenced and more distant mainland sanctuaries (e.g. Orokonui Ecosanctuary near Dunedin, and the Mokomoko Dryland Sanctuary in Central Otago) could be beneficial, given the increased vulnerability of small and sparsely forested islands to the effects of climate change (e.g. sea-level rise, coastal erosion, storm intensity; Macinnis-Ng et al. 2021). Such translocation may also facilitate the re-establishment of ‘lost’ ecological interactions and morphological diversity (e.g. Scarsbrook et al. 2021) specific to mainland and densely forested ecosystems. There is evidence of genetic sub-structuring (Scarsbrook et al. 2022) within the distribution of H. tohu, although this has been greatly reduced with the extinction of mainland South Island populations. Careful management, and possible further research should consider if individual populations are experiencing inbreeding depression and might benefit from genetic rescue – establishment of ‘new’ populations through interbreeding of individuals from different populations to increase genetic ‘fitness’ (i.e., adaptability). Conversely, continued maintenance of discrete lineages may also be appropriate if those lineages reflect local habitat adaptations or if pooled populations would comprise too few individuals to maintain the resulting genetic diversity due to genetic drift. Etymology.— The specific epithet was proposed by Dr Sharon Barcello-Gemmel, Rangatira of Te Ātiawa o Te Waka-a-Māui Trust, in recognition of the tupuna [ancestor] Tohu Kākahi. Tohu Kākahi was one of the two Parihaka prophets with whakapapa [genealogical] connections to Te Ātiawa – the iwi [tribe] with mana whenua [authority] over Ngāwhatu Kai Ponu [The Brothers], where the largest extant population occurs. Name used as noun in apposition., Published as part of Scarsbrook, Lachie, Walton, Kerry, Rawlence, Nicolas J. & Hitchmough, Rodney A., 2023, Revision of the New Zealand gecko genus Hoplodactylus, with the description of a new species, pp. 267-291 in Zootaxa 5228 (3) on pages 274-279, DOI: 10.11646/zootaxa.5228.3.3, http://zenodo.org/record/7532705, {"references": ["Gray, J. E. (1843) Descriptions of the reptiles and amphibians hitherto observed in New Zealand. In: Dieffenbach, E. (Ed.), Travels in New Zealand with contributions to the geography, geology, botany, and natural history of that country. Vol. 2. Murray, London, pp. 202 - 206.", "McCann, C. (1955) The lizards of New Zealand. Dominion Museum Bulletin, 17, 1 - 127.", "McCann, C. 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MSc Thesis, Victoria University of Wellington, Wellington, 106 pp.", "Frank, H. & Wilson, D. (2011) Distribution, status and conservation measures for lizards in limestone areas of South Canterbury, New Zealand. New Zealand Journal of Zoology, 38, 15 - 28. https: // doi. org / 10.1080 / 03014223.2010.520326", "Nielsen, S. V, Bauer, A. M., Jackman, T. R., Hitchmough, R. A. & Daugherty, C. H. (2011) New Zealand geckos (Diplodactylidae): Cryptic diversity in a post-Gondwanan lineage with trans-Tasman affinities. Molecular Phylogenetics and Evolution, 59, 1 - 22. https: // doi. org / 10.1016 / j. ympev. 2010.12.007", "Bell, T. P. & Herbert, S. M. (2012) Following up Duvaucel's gecko (Hoplodactylus duvaucelii) on Mana Island. Post-translocation monitoring 11 - 14 years on. In: Sanctuaries of New Zealand Workshop. EcoGecko Consultants, Inglewood, pp. 1 - 35.", "Garcia-Porta, J. & Ord, T. J. (2013) Key innovations and island colonization as engines of evolutionary diversification: a comparative test with the Australasian diplodactyloid geckos. Journal of Evolutionary Biology, 26, 2662 - 2680. https: // doi. org / 10.1111 / jeb. 12261", "Hitchmough, R., Anderson, P., Barr, B., Monks, J., Lettink, M., Reardon, J., Tocher, M. & Whitaker, T. (2013) Conservation status of New Zealand reptiles. 2012. In: New Zealand Threat Classification. Series 2. Department of Conservation, Wellington, pp. 1 - 16.", "Bell, T. (2014) Standardized common names for New Zealand reptiles. BioGecko, Wellington, 11 pp.", "Romijn, R. L., Nelson, N. J. & Monks, J. M. (2014) Forest geckos (Mokopirirakau ' Southern North Island') display diurno-nocturnal activity and are not reliant on retreats. New Zealand Journal of Zoology, 41, 103 - 113. https: // doi. org / 10.1080 / 03014223.2013.860041", "Heath, A. C. H. & Whitaker, A. H. (2015) Mites (Acari: Pterygosomatidae, Macronyssidae) taken from lizards intercepted at the New Zealand border. Systematic and Applied Acarology, 20, 739 - 756. https: // doi. org / 10.11158 / saa. 20.7.3", "Mockett, S. (2015) The evolution and diversity of parasites of New Zealand lizards. MSc thesis, University of Otago, Dunedin, 141 pp.", "Chapple, D. G. (2016 b) The future of New Zealand lizard research. In: Chapple, D. G. (Ed.), New Zealand Lizards. Springer, Cham, pp. 361 - 375. https: // doi. org / 10.1007 / 978 - 3 - 319 - 41674 - 8 _ 14", "Hitchmough, R. A., Patterson, G. B. & Chapple, D. G. (2016 b) Putting a name to diversity: Taxonomy of the New Zealand lizard fauna. In: Chapple, D. G. (Ed.), New Zealand Lizards. Springer, Cham, pp. 87 - 108. https: // doi. org / 10.1007 / 978 - 3 - 319 - 41674 - 8 _ 4", "Cree, A. & Hare, K. M. (2016) Reproduction and life history of New Zealand lizards. In: Chapple, D. G. (Ed.), New Zealand Lizards. Springer, Cham, pp. 169 - 206. https: // doi. org / 10.1007 / 978 - 3 - 319 - 41674 - 8 _ 7", "Hitchmough, R. A., Barr, B., Lettnik, M., Monks, J. M., Reardon, J. T., Tocher, M., van Winkel, D. & Rolfe, J. (2016 a) Conservation status of New Zealand reptiles. 2015. Department of Conservation, Wellington, 18 pp.", "Morgan-Richards, M., Hinlo, A. R., Smuts-Kennedy, C., Innes, J., Ji, W., Barry, M., Brunton, D. & Hitchmough, R. A. (2016) Identification of a rare gecko from North Island New Zealand, and genetic assessment of its probable origin: A novel mainland conservation priority? Journal of Herpetology, 50, 77 - 86. https: // doi. org / 10.1670 / 13 - 128", "Romijn, R. L. & Hartley, S. (2016) Trends in lizard translocations in New Zealand between 1988 and 2013. New Zealand Journal of Zoology, 43, 191 - 210. https: // doi. org / 10.1080 / 03014223.2016.1146311", "Towns, D. R., Hitchmough, R. A. & Perrott, J. (2016 b) Conservation of New Zealand lizards: A fauna not forgotten but undervalued? In: Chapple, D. G. (Ed.), New Zealand Lizards. Springer, Cham, pp. 293 - 320. https: // doi. org / 10.1007 / 978 - 3 - 319 - 41674 - 8 _ 11", "Worthy, T. H. (2016) A review of the fossil record of New Zealand lizards. In: Chapple, D. G. (Ed.), New Zealand Lizards. Springer, Cham, pp. 65 - 86. https: // doi. org / 10.1007 / 978 - 3 - 319 - 41674 - 8 _ 3", "Bell, T. P. & Herbert, S. M. (2017) Establishment of a self-sustaining population of a long-lived, slow-breeding gecko species (Diplodactylidae: Hoplodactylus duvaucelii) evident 15 years after translocation. Journal of Herpetology, 51, 37 - 46. https: // doi. org / 10.1670 / 15 - 106", "Bowers, L. (2017) Change over time on Mana Island. MA thesis, University of Otago, Dunedin, 90 pp.", "Knox, C. D., Jarvie, S., Easton, L. J. & Monks, J. M. (2017) Soft-release, but not cool winter temperatures, reduces post-translocation dispersal of jewelled geckos. Journal of Herpetology, 51, 490 - 496. https: // doi. org / 10.1670 / 16 - 078", "Lozito, T. P. & Tuan, R. S. (2017) Lizard tail regeneration as an instructive model of enhanced healing capabilities in an adult amniote. Connective Tissue Research, 58, 145 - 154. https: // doi. org / 10.1080 / 03008207.2016.1215444", "Sion, G. (2017) Foot-preference underlies bite-scar asymmetry in the gecko Ptyodactylus guttatus. Laterality, Series 1, 23, 129 - 151. https: // doi. org / 10.1080 / 1357650 X. 2017.1322097", "Stancher, G., Sovrano, V. A. & Vallortigara, G. (2018) Motor asymmetries in fishes, amphibians, and reptiles. Progress in Brain Research, 238, 33 - 56. https: // doi. org / 10.1016 / BS. PBR. 2018.06.002", "van Winkel, D., Baling, M. & Hitchmough, R. (2018) Reptiles and amphibians of New Zealand. Auckland University Press, Auckland, 712 pp.", "Skipwith, P. L., Bi, K. & Oliver, P. M. (2019) Relicts and radiations: phylogenomics of an Australasian lizard clade with east Gondwanan origins (Gekkota: Diplodactyloidea). Molecular Phylogenetics and Evolution, 140, 106589. https: // doi. org / 10.1016 / j. ympev. 2019.106589", "Florence-Bennett, B. J. (2020) Assessing bird predation on New Zealand's lizard fauna using lizard-mimicking replicas. MSc thesis, Victoria University of Wellington, 119 pp.", "Glynne, E., Daza, J. D. & Bauer, A. M. (2020) Surface sculpturing in the skull of gecko lizards (Squamata: Gekkota). Biological Journal of the Linnean Society, 131, 801 - 813. https: // doi. org / 10.1093 / biolinnean / blaa 144", "Herbert, S. M. (2020) Is habitat enhancement a viable strategy for conserving New Zealand's endemic lizards? PhD thesis, Victoria University of Wellington, Wellington, 274 pp.", "Price, S. J., Grayson, K. L., Gartrell, B. D. & Nelson, N. J. (2020) Survival and growth of tuatara Sphenodon punctatus following translocation from the Cook Strait to warmer locations in their historic range. Oryx, 54, 222 - 233. https: // doi. org / 10.1017 / S 003060531800008 X", "Scarsbrook, L., Sherratt, E., Hitchmough, R. A. & Rawlence, N. J. (2021) Skeletal variation in extant species enables systematic identification of New Zealand's large, subfossil diplodactylids. BMC ecology and evolution, 21, 67. https: // doi. org / 10.1186 / s 12862 - 021 - 01808 - 7", "Scarsbrook, L., Verry, A. J. F., Walton, K., Hitchmough, R. A. & Rawlence, N. J. (2022) Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus Hoplodactylus. Molecular Ecology, 1 - 21. [early view] https: // doi. org / 10.1111 / mec. 16434", "Chrapliwy, P. S., Smith, H. M. & Grant, C. (1961) The systematic status of the Geckonid lizard genera Gehyra, Peropus, Hoplodactylus and Naultinus. Herpetologica, 17, 5 - 12.", "Jewell, T. (2008) A photographic guide to reptiles and amphibians of New Zealand. New Holland Publishers Ltd, Auckland, 143 pp.", "Fitzinger, L. (1843) Systema reptilium, fasciculus primus: Amblyglossae. Braumuller et Seidel, Vindobonae, 106 pp. https: // doi. org / 10.5962 / bhl. title. 4694", "Hitchmough, R. A., Barr, B., Knox, C., Lettink, M., Monks, J. M., Patterson, G. B., Reardon, J. T., van Winkel, D., Rolfe, J. & Michel, P. (2021 a) Conservation status of New Zealand reptiles. 2021. Department of Conservation, Wellington, 27 pp.", "Mayr, E. (1942) Systematics and the Origin of Species. Columbia University, New York, New York, 367 pp.", "Brennan, I. G., Bauer, A. M. & Jackman, T. R. (2016) Mitochondrial introgression via ancient hybridization, and systematics of the Australian endemic pygopodid gecko genus Delma. Molecular Phylogenetics and Evolution, 94, 577 - 590. https: // doi. org / 10.1016 / j. ympev. 2015.10.005", "Leache, A. D. & Cole, C. J. (2006) Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology. Molecular Ecology, 16, 1035 - 1054. https: // doi. org / 10.1111 / j. 1365 - 294 X. 2006.03194. x", "Olave, M., Martinez, L. E., Avila, L. J., Sites, J. W. & Morando, M. (2011) Evidence of hybridization in the Argentinean lizards Liolaemus gracilis and Liolaemus bibronii (Iguania: Liolaemini): an integrative approach based on genes and morphology. Molecular Phylogenetics and Evolution, 61, 381 - 391. https: // doi. org / 10.1016 / j. ympev. 2011.07.006", "Gr
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- 2023
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24. Artificial Intelligence in Ovarian Cancer Histopathology: A Systematic Review
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Breen, Jack, Allen, Katie, Zucker, Kieran, Adusumilli, Pratik, Scarsbrook, Andy, Hall, Geoff, Orsi, Nicolas M., and Ravikumar, Nishant
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FOS: Computer and information sciences ,Computer Science - Machine Learning ,Artificial Intelligence (cs.AI) ,Computer Science - Artificial Intelligence ,Image and Video Processing (eess.IV) ,FOS: Electrical engineering, electronic engineering, information engineering ,Electrical Engineering and Systems Science - Image and Video Processing ,Machine Learning (cs.LG) - Abstract
Purpose - To characterise and assess the quality of published research evaluating artificial intelligence (AI) methods for ovarian cancer diagnosis or prognosis using histopathology data. Methods - A search of PubMed, Scopus, Web of Science, CENTRAL, and WHO-ICTRP was conducted up to 19/05/2023. The inclusion criteria required that research evaluated AI on histopathology images for diagnostic or prognostic inferences in ovarian cancer. The risk of bias was assessed using PROBAST. Information about each model of interest was tabulated and summary statistics were reported. PRISMA 2020 reporting guidelines were followed. Results - 1573 records were identified, of which 45 were eligible for inclusion. There were 80 models of interest, including 37 diagnostic models, 22 prognostic models, and 21 models with other diagnostically relevant outcomes. Models were developed using 1-1375 slides from 1-776 ovarian cancer patients. Model outcomes included treatment response (11/80), malignancy status (10/80), stain quantity (9/80), and histological subtype (7/80). All models were found to be at high or unclear risk of bias overall, with most research having a high risk of bias in the analysis and a lack of clarity regarding participants and predictors in the study. Research frequently suffered from insufficient reporting and limited validation using small sample sizes. Conclusion - Limited research has been conducted on the application of AI to histopathology images for diagnostic or prognostic purposes in ovarian cancer, and none of the associated models have been demonstrated to be ready for real-world implementation. Key aspects to help ensure clinical translation include more transparent and comprehensive reporting of data provenance and modelling approaches, as well as improved quantitative performance evaluation using cross-validation and external validations.
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- 2023
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25. TypeScript's Evolution: An Analysis of Feature Adoption Over Time
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Scarsbrook, Joshua D., Utting, Mark, and Ko, Ryan K. L.
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Software Engineering (cs.SE) ,FOS: Computer and information sciences ,Computer Science - Software Engineering - Abstract
TypeScript is a quickly evolving superset of JavaScript with active development of new features. Our paper seeks to understand how quickly these features are adopted by the developer community. Existing work in JavaScript shows the adoption of dynamic language features can be a major hindrance to static analysis. As TypeScript evolves the addition of features makes the underlying standard more and more difficult to keep up with. In our work we present an analysis of 454 open source TypeScript repositories and study the adoption of 13 language features over the past three years. We show that while new versions of the TypeScript compiler are aggressively adopted by the community, the same cannot be said for language features. While some experience strong growth others are rarely adopted by projects. Our work serves as a starting point for future study of the adoption of features in TypeScript. We also release our analysis and data gathering software as open source in the hope it helps the programming languages community.
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- 2023
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26. Large floodplain river restoration in New Zealand: synthesis and critical evaluation to inform restoration planning and research
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Jonathan M. Abell, Michael A. Pingram, Deniz Özkundakci, Bruno O. David, Mike Scarsbrook, Thomas Wilding, Alicia Williams, Matt Noble, James Brasington, and Alton Perrie
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Global and Planetary Change - Abstract
New Zealand (NZ) has a diversity of large river ecosystems that provide essential ecosystem services but are impaired by multiple ecological impacts. River restoration is an active field worldwide and there is good potential for river restoration practitioners in NZ to draw on lessons from elsewhere, although there is also a need to tailor approaches to national and local contexts. Here, we provide a critical review of large floodplain river restoration to guide environmental management in NZ and inform research and management priorities. The review is structured using a driver-pressure-state-impact-response framework, with a focus on responses, i.e. large river restoration methods. Thirty-one river restoration methods aligned with 14 broad restoration goals were evaluated collaboratively and semi-quantitatively. Evaluation outcomes are presented to inform regional and national scale restoration planning. Recommendations were identified to address eight key knowledge or policy gaps: (1) understanding cumulative impacts facing large river systems, (2) prioritising restoration measures at the landscape-scale, (3) promoting lateral connectivity in large river floodplains, (4) incorporating knowledge of geomorphology into river management, (5) enhancing understanding of cultural priorities and community aspirations, (6) assessing how costs and benefits of river restoration vary among timescales, (7) understanding the feasibility of restoration methods that have received limited application in NZ and (8) improving protection of threatened native fish species.
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- 2022
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27. The Global Reading Room: Performing a Gastric Emptying Study
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Pradeep Bhambhvani, Andrew Scarsbrook, Hans Van der Wall, and Katherine Zukotynski
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Radiology, Nuclear Medicine and imaging ,General Medicine - Published
- 2023
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28. 'Squash, tilt, drag, split, turn...' An intervention study examining children's collaborative talk and reasoning about shape, space and measure
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Scarsbrook, Jane
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geometry ,intervention study ,primary education ,collaborative learning ,reasoning ,shape, space and measure ,mathematics education ,imagination ,metaphor - Abstract
The aim of this thesis is to evaluate the effect of collaborative work on primary-age children’s reasoning about shape, space and measure. Children’s early development in these areas of mathematics has been well researched but the difficulties older children experience are less well charted. Method: An intervention study was carried out with two Year 5 classes in a South London primary school using a naturalistic experimental design with two parallel classes as the intervention and control groups. The intervention class undertook two iterations of group work while the control class worked individually across the two sessions. An innovative pre- to post-test measure was developed using the Rasch Analysis partial credit model. This consisted of two sets of six similar and overlapping think-aloud tasks. The design of the group work was informed by both sociocultural and socio-cognitive conflict theory: ground rules for talk were used in the intervention class and the children were grouped in triads with differing ideas (elicited from their pre-test responses). Novel features were included to increase the likelihood of all children encountering challenge to their initial ideas: a) the children were prompted to reflect on the certainty of their joint or individual answers at the end of the first session; b) the children all had the chance to consult written clues in the second session, at the cost of a point per clue. Analysis: Quantitative comparison of the children’s progress from pre- to post-test was complemented with qualitative analysis of the children’s use of language across the study. Transcripts of the children talking about the shape, space and measurement tasks were coded for imaginative expressions to explore whether imaginative forms were associated with more sophisticated reasoning about shape, space and measure. The children’s group talk was coded for exploratory features of language to evaluate the impact on the children’s reasoning of the prompt to reflect on the certainty of their joint responses. Findings: The children working in groups made significantly more progress than the children working alone from pre- to post-test, as hypothesised, and they were more effective in their decisions about whether to seek help in the form of written clues than children working alone. Following the prompt to reflect on their group answers, there were changes in the observed language of the intervention groups. While the overall use of exploratory features: “because”, “I think”, “I agree/disagree” and modal verbs remained similar from session one to session two, there was a significant increase in the use of modal verbs following the prompt (p < .05). Swift surface-level agreements were probed further after a group consensus had been reached. Using a grounded approach, the children’s imaginative expressions across the study were coded and three categories identified: movement, manipulation or decomposition. Children working with peers made more progress and increased their use of imaginative expressions from pre- to post-test by comparison with the children working alone. Temporal analysis of the children’s talk across the study revealed common examples of imaginative work that supported the development of more sophisticated reasoning. For example, imagining “splitting” and “halving” objects served as a heuristic bridge towards inferring length and finding the difference. Similarly, by imagining “turning” and “squashing” familiar shapes, children began to create axioms about the properties of shape beyond iconic examples and orientations. The partial credit model used to measure children’s progress in this study increases our knowledge about the incremental steps that children make in their understanding about geometry and measurement in the upper primary years. By revealing the imaginative language tools the children used to probe their existing reasoning models, this study highlights the importance of children articulating their imaginative work in maths with peers.
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- 2022
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29. atomCAT2 - A multicentre study of overall survival, locoregional control and distant metastasis in anal cancer utilising distributed learning
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Theophanous, Stelios, Appelt, Ane, Wee, Leonard, Lønne, Per-Ivar, Malinen, Eirik, Choudhury, Ananya, Gilbert, Alexandra, Berbee, Maaike, Guren, Marianne, Dekker, Andre, Scarsbrook, Andrew, and Sebag-Montefiore, David
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FOS: Computer and information sciences ,Oncology ,Bioinformatics ,Neoplasms ,Medicine and Health Sciences ,Medical Specialties ,Life Sciences ,Diseases - Abstract
The atomCAT2 project will analyse retrospective data from anal cancer patients treated with (chemo)radiotherapy across institutions in the UK and internationally. The study aims to develop and validate outcome prediction models using baseline patient characteristics and simple treatment-related factors. It will use distributing learning methodology, which facilitates multi-centre data analysis without individual patient data leaving the local data repository. This will allow us to examine which factors predict for effect of radiotherapy on the primary cancer, and which factors predict for metastatic spread. Ultimately, this could aid in the design of better trials for anal cancer as well as improve treatment for future patients.
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- 2022
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30. PETER TSCHMUCK: Einführung in die Kulturbetriebslehre. Springer VS. Wiesbaden 2020, 160 Seiten
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Sarah Scarsbrook
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General Earth and Planetary Sciences ,General Environmental Science - Published
- 2021
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31. Chest pain mimicking pulmonary embolism may be a common presentation of COVID‐19 in ambulant patients without other typical features of infection
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Dennis McGonagle, Joel Rl Klassen, Charlie Bridgewood, Stephanie R Harrison, Andrew Scarsbrook, and Helena Marzo-Ortega
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Male ,0301 basic medicine ,Chest Pain ,medicine.medical_specialty ,Computed Tomography Angiography ,noncardiac chest pain ,infectious disease ,Infarction ,Atelectasis ,030204 cardiovascular system & hematology ,Chest pain ,Ground-glass opacity ,Diagnosis, Differential ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Internal Medicine ,medicine ,Humans ,Lung ,Retrospective Studies ,Pneumonitis ,Clinical Audit ,business.industry ,COVID-19 ,Original Articles ,Middle Aged ,thromboembolism ,medicine.disease ,Thrombosis ,radiology ,Pulmonary embolism ,Pneumonia ,030104 developmental biology ,Female ,Original Article ,medicine.symptom ,Pulmonary Embolism ,business - Abstract
Background Radiological and pathological studies in severe COVID‐19 pneumonia (SARS‐CoV‐2) have demonstrated extensive pulmonary immunovascular thrombosis and infarction. This study investigated whether these focal changes may present with chest pain mimicking pulmonary emoblism (PE) in ambulant patients. Methods CTPAs from outpatients presenting with chest pain to Leeds Teaching Hospital NHS Trust 1st March to 31 May 2020 (n = 146) and 2019 (n = 85) were compared. Regions of focal ground glass opacity (GGO), consolidation and/or atelectasis (parenchymal changes) were determined, and all scans were scored using British Society for Thoracic Imaging (BSTI) criteria for COVID‐19, and the 2020 cohort was offered SARS‐CoV‐2 antibody testing. Results Baseline demographic and clinical data were similar between groups with absence of fever, normal lymphocytes and marginally elevated CRP and D‐Dimer values. Evidence of COVID‐19 or parenchymal changes was observed in 32.9% (48/146) of cases in 2020 compared to 16.5% (14/85) in 2019 (P = 0.007). 11/146 (7.5%) patients met BSTI criteria for COVID‐19 in 2020 compared with 0/14 in 2019 (P = 0.008). 3/39 patients tested had detectable COVID‐19 antibodies (2 with parenchymal changes and 1 with normal parenchyma) however 0/6 patients whose CTPA met BSTI criteria “likely/suspicious for COVID‐19” and attended antibody testing were SARS‐CoV‐2 antibody positive. Conclusions 32.8% ambulatory patients with suspected PE in 2020 had parenchymal changes with 7.5% diagnosed as COVID‐19 infection by imaging criteria, despite the absence of other COVID‐19 symptoms. These findings suggest that localized COVID‐19 pneumonitis with immunothrombosis occurs distal to the bronchiolar arteriolar circulation, causing pleural irritation and chest pain without viraemia, accounting for the lack of fever and systemic symptoms.
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- 2021
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32. Dynamic feature learning for COVID-19 segmentation and classification
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Xiaoqin Zhang, Runhua Jiang, Pengcheng Huang, Tao Wang, Mingjun Hu, Andrew F. Scarsbrook, and Alejandro F. Frangi
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Health Informatics ,Computer Science Applications - Abstract
Since December 2019, coronavirus SARS-CoV-2 (COVID-19) has rapidly developed into a global epidemic, with millions of patients affected worldwide. As part of the diagnostic pathway, computed tomography (CT) scans are used to help patient management. However, parenchymal imaging findings in COVID-19 are non-specific and can be seen in other diseases. In this work, we propose to first segment lesions from CT images, and further, classify COVID-19 patients from healthy persons and common pneumonia patients. In detail, a novel Dynamic Fusion Segmentation Network (DFSN) that automatically segments infection-related pixels is first proposed. Within this network, low-level features are aggregated to high-level ones to effectively capture context characteristics of infection regions, and high-level features are dynamically fused to model multi-scale semantic information of lesions. Based on DFSN, Dynamic Transfer-learning Classification Network (DTCN) is proposed to distinguish COVID-19 patients. Within DTCN, a pre-trained DFSN is transferred and used as the backbone to extract pixel-level information. Then the pixel-level information is dynamically selected and used to make a diagnosis. In this way, the pre-trained DFSN is utilized through transfer learning, and clinical significance of segmentation results is comprehensively considered. Thus DTCN becomes more sensitive to typical signs of COVID-19. Extensive experiments are conducted to demonstrate effectiveness of the proposed DFSN and DTCN frameworks. The corresponding results indicate that these two models achieve state-of-the-art performance in terms of segmentation and classification.
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- 2022
33. Exploratory Analysis of Serial
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Kavi, Fatania, Russell, Frood, Marcus, Tyyger, Garry, McDermott, Sharon, Fernandez, Gary C, Shaw, Marjorie, Boissinot, Daniela, Salvatore, Luisa, Ottobrini, Irvin, Teh, John, Wright, Marc A, Bailey, Joanna, Koch-Paszkowski, Jurgen E, Schneider, David L, Buckley, Louise, Murray, Andrew, Scarsbrook, Susan C, Short, and Stuart, Currie
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Anti-1-amino-3
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- 2022
34. Evaluation of a tertiary centre specialist adrenal MDT: The first 900 patients
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Louisa Child, Rebecca Sagar, Sheila Fraser, Emma Collins, Russell Frood, Andrew Scarsbrook, and Afroze Abbas
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- 2022
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35. Mild autonomous cortisol secretion in patients with adrenal incidentalomas and raised cardiovascular risk
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Rebecca Sagar, Sheila Fraser, Emma Collins, Russell Frood, Andrew Scarsbrook, Stewart Paul M, and Afroze Abbas
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- 2022
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36. PO-1067 Exploratory analysis of serial 18F-Fluciclovine PET and mpMRI during chemoradiation for glioblastoma
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Louise Murray, R. Frood, Stuart Currie, M. Tyyger, David L. Buckley, K. Fatania, Susan C Short, Andrew Scarsbrook, and Sharon Fernandez
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Oncology ,medicine.medical_specialty ,business.industry ,Internal medicine ,medicine ,Radiology, Nuclear Medicine and imaging ,Hematology ,Exploratory analysis ,business ,medicine.disease ,Glioblastoma - Published
- 2021
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37. Effect of 18F-Fluciclovine Positron Emission Tomography on the Management of Patients With Recurrence of Prostate Cancer: Results From the FALCON Trial
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Andrew F. Scarsbrook, David Bottomley, Eugene J. Teoh, Kevin M. Bradley, Heather Payne, Asim Afaq, Jamshed Bomanji, Nicholas van As, Sue Chua, Peter Hoskin, Anthony Chambers, Gary J. Cook, Victoria S. Warbey, Sai Han, Hing Y. Leung, Albert Chau, Matthew P. Miller, Fergus V. Gleeson, Gerard Andrade, Philip Camilieri, Katherine Hyde, Ruth Macpherson, Neel Patel, Ami Sabharwal, Manil Subesinghe, and Maria Tsakok
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First episode ,Biochemical recurrence ,Cancer Research ,medicine.medical_specialty ,Radiation ,business.industry ,medicine.medical_treatment ,Brachytherapy ,Salvage therapy ,medicine.disease ,030218 nuclear medicine & medical imaging ,Radiation therapy ,03 medical and health sciences ,Prostate-specific antigen ,Prostate cancer ,0302 clinical medicine ,Oncology ,030220 oncology & carcinogenesis ,medicine ,Radiology, Nuclear Medicine and imaging ,Radiology ,Radiation treatment planning ,business - Abstract
Purpose\ud\udEarly and accurate localization of lesions in patients with biochemical recurrence (BCR) of prostate cancer may guide salvage therapy decisions. The present study, 18F-Fluciclovine PET/CT in biochemicAL reCurrence Of Prostate caNcer (FALCON; NCT02578940), aimed to evaluate the effect of 18F-fluciclovine on management of men with BCR of prostate cancer.\udMethods and Materials\ud\udMen with a first episode of BCR after curative-intent primary therapy were enrolled at 6 UK sites. Patients underwent 18F-fluciclovine positron emission tomography/computed tomography (PET/CT) according to standardized procedures. Clinicians documented management plans before and after scanning, recording changes to treatment modality as major and changes within a modality as other. The primary outcome measure was record of a revised management plan postscan. Secondary endpoints were evaluation of optimal prostate specific antigen (PSA) threshold for detection, salvage treatment outcome assessment based on 18F-fluciclovine-involvement, and safety.\udResults\ud\ud18F-Fluciclovine was well tolerated in the 104 scanned patients (median PSA = 0.79 ng/mL). Lesions were detected in 58 out of 104 (56%) patients. Detection was broadly proportional to PSA level; ≤1 ng/mL, 1 out of 3 of scans were positive, and 93% scans were positive at PSA >2.0 ng/mL. Sixty-six (64%) patients had a postscan management change (80% after a positive result). Major changes (43 out of 66; 65%) were salvage or systemic therapy to watchful waiting (16 out of 66; 24%); salvage therapy to systemic therapy (16 out of 66; 24%); and alternative changes to treatment modality (11 out of 66, 17%). The remaining 23 out of 66 (35%) management changes were modifications of the prescan plan: most (22 out of 66; 33%) were adjustments to planned brachytherapy/radiation therapy to include a 18F-fluciclovine-guided boost. Where 18F-fluciclovine guided salvage therapy, the PSA response rate was higher than when 18F-fluciclovine was not involved (15 out of 17 [88%] vs 28 out of 39 [72%]).\udConclusions\ud\ud18F-Fluciclovine PET/CT located recurrence in the majority of men with BCR, frequently resulting in major management plan changes. Incorporating 18F-fluciclovine PET/CT into treatment planning may optimize targeting of recurrence sites and avoid futile salvage therapy.
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- 2020
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38. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus
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Lachie Scarsbrook, Alexander J. F. Verry, Kerry Walton, Rodney A. Hitchmough, and Nicolas J. Rawlence
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Genetics ,Ecology, Evolution, Behavior and Systematics - Abstract
Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898-2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-computed tomography reconstructions. All "large gecko" specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue-derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.
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- 2022
39. Erratum: Revision of the New Zealand gecko genus Hoplodactylus, with the description of a new species. Zootaxa 5228 (3): 267–291
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LACHIE SCARSBROOK, KERRY WALTON, NICOLAS J. RAWLENCE, and RODNEY A. HITCHMOUGH
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Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics - Published
- 2023
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40. Additional file 1 of Development and validation of prognostic models for anal cancer outcomes using distributed learning: protocol for the international multi-centre atomCAT2 study
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Theophanous, Stelios, Lønne, Per-Ivar, Choudhury, Ananya, Berbee, Maaike, Dekker, Andre, Dennis, Kristopher, Dewdney, Alice, Gambacorta, Maria Antonietta, Gilbert, Alexandra, Guren, Marianne Grønlie, Holloway, Lois, Jadon, Rashmi, Kochhar, Rohit, Mohamed, Ahmed Allam, Muirhead, Rebecca, Parés, Oriol, Raszewski, Lukasz, Roy, Rajarshi, Scarsbrook, Andrew, Sebag-Montefiore, David, Spezi, Emiliano, Spindler, Karen-Lise Garm, van Triest, Baukelien, Vassiliou, Vassilios, Malinen, Eirik, Wee, Leonard, and Appelt, Ane L.
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Additional file 1: Appendix 1. Data dictionary
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- 2022
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41. Additional file 2 of Development and validation of prognostic models for anal cancer outcomes using distributed learning: protocol for the international multi-centre atomCAT2 study
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Theophanous, Stelios, Lønne, Per-Ivar, Choudhury, Ananya, Berbee, Maaike, Dekker, Andre, Dennis, Kristopher, Dewdney, Alice, Gambacorta, Maria Antonietta, Gilbert, Alexandra, Guren, Marianne Grønlie, Holloway, Lois, Jadon, Rashmi, Kochhar, Rohit, Mohamed, Ahmed Allam, Muirhead, Rebecca, Parés, Oriol, Raszewski, Lukasz, Roy, Rajarshi, Scarsbrook, Andrew, Sebag-Montefiore, David, Spezi, Emiliano, Spindler, Karen-Lise Garm, van Triest, Baukelien, Vassiliou, Vassilios, Malinen, Eirik, Wee, Leonard, and Appelt, Ane L.
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Additional file 2: Appendix 2. Specification of secondary models
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- 2022
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42. Plan2Defend: AI Planning for Cybersecurity in Smart Grids
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Taejun Choi, Ryan K L Ko, Tapan Saha, Joshua Scarsbrook, Abigail MY Koay, Shunyao Wang, Wenlu Zhang, and Connor St Clair
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- 2021
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43. Can weekly ‘foot alerts’ using a bespoke mobile app improve patient diabetic foot care knowledge and practices in Kuwait
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Kay Scarsbrook Khan
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- 2021
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44. Protocol for a MULTI-centre feasibility study to assess the use of99mTc-sestaMIBI SPECT/CT in the diagnosis of kidney tumours (MULTI-MIBI study)
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Hannah Warren, Thomas Wagner, Michael A Gorin, Steven Rowe, Beverley Fiona Holman, Deborah Pencharz, Soha El-Sheikh, Ravi Barod, Prasad Patki, Faiz Mumtaz, Axel Bex, Veeru Kasivisvanathan, Caroline M Moore, Nicholas Campain, Jon Cartledge, Andrew Scarsbrook, Fahim Hassan, Tim S O'Brien, Grant D Stewart, Iosif Mendichovszky, Sabina Dizdarevic, Ammar Alanbuki, William H Wildgoose, Tze Wah, Cecilia Vindrola-Padros, Elena Pizzo, Hakim-Moulay Dehbi, Paula Lorgelly, Kurinchi Gurusamy, Mark Emberton, and Maxine G B Tran
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General Medicine - Abstract
IntroductionThe incidence of renal tumours is increasing and anatomic imaging cannot reliably distinguish benign tumours from renal cell carcinoma. Up to 30% of renal tumours are benign, with oncocytomas the most common type. Biopsy has not been routinely adopted in many centres due to concerns surrounding non-diagnostic rate, bleeding and tumour seeding. As a result, benign masses are often unnecessarily surgically resected.99mTc-sestamibi SPECT/CT has shown high diagnostic accuracy for benign renal oncocytomas and other oncocytic renal neoplasms of low malignant potential in single-centre studies. The primary aim of MULTI-MIBI is to assess feasibility of a multicentre study of99mTc-sestamibi SPECT/CT against a reference standard of histopathology from surgical resection or biopsy. Secondary aims of the study include obtaining estimates of99mTc-sestamibi SPECT/CT sensitivity and specificity and to inform the design and conduct of a future definitive trial.Methods and analysisA feasibility prospective multicentre study of participants with indeterminate, clinical T1 renal tumours to undergo99mTc-sestamibi SPECT/CT (index test) compared with histopathology from biopsy or surgical resection (reference test). Interpretation of the index and reference tests will be blinded to the results of the other. Recruitment rate as well as estimates of sensitivity, specificity, positive and negative predictive value will be reported. Semistructured interviews with patients and clinicians will provide qualitative data to inform onward trial design and delivery. Training materials for99mTc-sestamibi SPECT/CT interpretation will be developed, assessed and optimised. Early health economic modelling using a decision analytic approach for different diagnostic strategies will be performed to understand the potential cost-effectiveness of99mTc-sestamibi SPECT/CT.Ethics and disseminationEthical approval has been granted (UK HRA REC 20/YH/0279) protocol V.5.0 dated 21/6/2022. Study outputs will be presented and published nationally and internationally.Trial registration numberISRCTN12572202.
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- 2023
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45. Reirradiation Options for Previously Irradiated Prostate cancer (RO-PIP): Feasibility study investigating toxicity outcomes following reirradiation with stereotactic body radiotherapy (SBRT) versus high-dose-rate brachytherapy (HDR-BT)
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Jim Zhong, Sarah Brown, Maria Serra, Pam Shuttleworth, Peter Bownes, Christopher Thompson, Rachel Reed, Kimberley Reeves, Michael Dubec, Damien McHugh, Cynthia Eccles, Robert Chuter, Yat Man Tsang, N Jane Taylor, Catharine West, David Buckley, Andrew Scarsbrook, Ananya Choudhury, Peter Hoskin, and Ann Henry
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Male ,Proteomics ,Radiosurgery/adverse effects ,Manchester Cancer Research Centre ,ResearchInstitutes_Networks_Beacons/mcrc ,Brachytherapy ,Prostatic Neoplasms ,Radiotherapy Dosage ,Brachytherapy/adverse effects ,Prostatic Neoplasms/pathology ,General Medicine ,Radiosurgery ,Re-Irradiation ,Magnetic resonance imaging ,Prostate disease ,Humans ,Feasibility Studies ,Prospective Studies ,RADIOTHERAPY - Abstract
IntroductionRadiotherapy is the most common curative treatment for non-metastatic prostate cancer; however, up to 13% of patients will develop local recurrence within 10 years. Patients can undergo further and potentially curative treatment including salvage surgery, brachytherapy (BT), external beam radiotherapy, high-intensity focused ultrasound and cryotherapy. Systematic review shows that high-dose-rate (HDR) BT and stereotactic body radiotherapy (SBRT) have the best outcomes in terms of biochemical control and lowest side effects. The reirradiation options for previously irradiated prostate cancer (RO-PIP) trial aims to determine the feasibility of recruitment to a trial randomising patients to salvage HDR-BT or SBRT and provide prospective data on patient recorded toxicity outcomes that will inform a future phase III trial.Methods and analysisThe primary endpoint of the RO-PIP feasibility study is to evaluate the patient recruitment potential over 2 years to a trial randomising to either SBRT or HDR-BT for patients who develop local recurrence of prostate cancer following previous radiation therapy. The aim is to recruit 60 patients across 3 sites over 2 years and randomise 1:1 to SBRT or HDR-BT. Secondary objectives include recording clinician and patient-reported outcome measures to evaluate treatment-related toxicity. In addition, the study aims to identify potential imaging, genomic and proteomic biomarkers that are predictive of toxicity and outcome based on hypoxia status, a prognostic marker of prostate cancer.Ethics and disseminationThis study has been approved by the Yorkshire and The Humber—Bradford Leeds Research Ethics Committee (Reference: 21/YH/0305, IRAS: 297060, January 2022). The results will be presented in national and international conferences, published in peer-reviewed journals and will be communicated to relevant stakeholders. A plain English report will be shared with the study participants, patients’ organisations and media.Trial registration numberISRCTN 12238218 (Amy Ackroyd NIHR CPMS Team).
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- 2022
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46. Topological analysis of a bacterial DedA protein associated with alkaline tolerance and antimicrobial resistance
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Hollie L. Scarsbrook, Roman Urban, Bree R. Streather, Alexandra Moores, and Christopher Mulligan
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biology ,Chemistry ,Escherichia coli Proteins ,Membrane Proteins ,Transporter ,medicine.disease_cause ,biology.organism_classification ,Topology ,Microbiology ,Oligomer ,QR ,Anti-Bacterial Agents ,chemistry.chemical_compound ,Bacterial Proteins ,Drug Resistance, Bacterial ,Mutation ,medicine ,Efflux ,QP517 ,Escherichia coli ,Integral membrane protein ,Bacteria ,Function (biology) ,Cysteine - Abstract
Maintaining membrane integrity is of paramount importance to the survival of bacteria as the membrane is the site of multiple crucial cellular processes including energy generation, nutrient uptake and antimicrobial efflux. The DedA family of integral membrane proteins are widespread in bacteria and are associated with maintaining the integrity of the membrane. In addition, DedA proteins have been linked to resistance to multiple classes of antimicrobials in various microorganisms. Therefore, the DedA family are attractive targets for the development of new antibiotics. Despite DedA family members playing a key physiological role in many bacteria, their structure, function and physiological role remain unclear. To help illuminate the structure of the bacterial DedA proteins, we performed substituted cysteine accessibility method (SCAM) analysis on the most comprehensively characterized bacterial DedA protein, YqjA from Escherichia coli . By probing the accessibility of 15 cysteine residues across the length of YqjA using thiol reactive reagents, we mapped the topology of the protein. Using these data, we experimentally validated a structural model of YqjA generated using evolutionary covariance, which consists of an α-helical bundle with two re-entrant hairpin loops reminiscent of several secondary active transporters. In addition, our cysteine accessibility data suggest that YqjA forms an oligomer wherein the protomers are arranged in a parallel fashion. This experimentally verified model of YqjA lays the foundation for future work in understanding the function and mechanism of this interesting and important family.
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- 2021
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47. Rapid radiation of Southern Ocean shags in response to receding sea ice
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Norman Ratcliffe, Alexander T. Salis, Tania M. King, Peter G. Ryan, Petra Quillfeldt, Nicolas J. Rawlence, Richard A. Phillips, Charlotte E. Till, Timothée R. Cook, Lachie Scarsbrook, Ludovic Dutoit, Luciano Calderón, Jonathan M. Waters, Charles-André Bost, Juan F. Masello, Lisa J. Nupen, Martyn Kennedy, and Hamish G. Spencer
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Geography ,Taxon ,geography.geographical_feature_category ,biology ,Ecology ,biology.animal ,Sea ice ,Biological dispersal ,Marine ecosystem ,Glacial period ,Circumpolar star ,Seabird ,Local adaptation - Abstract
AimUnderstanding how wild populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. The blue-eyed shags (Leucocarbospp.) represent a paradoxical Southern Ocean seabird radiation; a circumpolar distribution implies strong dispersal capacity yet their speciose nature suggests local adaptation and isolation. Here we use genetic tools in an attempt to resolve this paradox.LocationSouthern Ocean.Taxa17 species and subspecies of blue-eyed shags (Leucocarbospp.) across the geographical distribution of the genus.MethodsHere we use mitochondrial and nuclear sequence data to conduct the first global genetic analysis of this group using a temporal phylogenetic framework to test for rapid speciation.ResultsOur analysis reveals remarkably shallow evolutionary histories among island-endemic lineages, consistent with a recent high-latitude circumpolar radiation. This rapid sub-Antarctic expansion contrasts with significantly deeper lineages detected in more temperate regions such as South America and New Zealand that may have acted as glacial refugia. The dynamic history of high-latitude expansions is further supported by ancestral demographic and biogeographic reconstructions.Main conclusionsThe circumpolar distribution of blue-eyed shags, and their highly dynamic evolutionary history, potentially makeLeucocarboa strong sentinel of past and ongoing Southern Ocean ecosystem change given their sensitivity to climatic impacts.
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- 2021
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48. Cell proliferation detected using [18F]FLT PET/CT as an early marker of abdominal aortic aneurysm
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Andrew Scarsbrook, John D Wright, Michael Shires, Charalampos Tsoumpas, Christopher Cawthorne, Marc A. Bailey, Lucinda J L Craggs, Stephen J. Archibald, Ping He, Joanna Koch-Paszkowski, Richa Gandhi, and Juozas Domarkas
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medicine.medical_specialty ,Apolipoprotein B ,medicine.medical_treatment ,Urology ,030204 cardiovascular system & hematology ,Vascular biology ,Concentrative nucleoside transporter ,03 medical and health sciences ,aneurysms ,0302 clinical medicine ,vascular imaging ,medicine ,Radiology, Nuclear Medicine and imaging ,Saline ,PET-CT ,biology ,medicine.diagnostic_test ,Cell growth ,business.industry ,molecular imaging ,medicine.disease ,Angiotensin II ,Abdominal aortic aneurysm ,PET ,pre-clinical imaging ,Positron emission tomography ,030220 oncology & carcinogenesis ,cardiovascular system ,biology.protein ,Cardiology and Cardiovascular Medicine ,business - Abstract
Background Abdominal aortic aneurysm (AAA) is a focal aortic dilatation progressing towards rupture. Non-invasive AAA-associated cell proliferation biomarkers are not yet established. We investigated the feasibility of the cell proliferation radiotracer, fluorine-18-fluorothymidine ([18F]FLT) with positron emission tomography/computed tomography (PET/CT) in a progressive pre-clinical AAA model (angiotensin II, AngII infusion). Methods and Results Fourteen-week-old apolipoprotein E-knockout (ApoE−/−) mice received saline or AngII via osmotic mini-pumps for 14 (n = 7 and 5, respectively) or 28 (n = 3 and 4, respectively) days and underwent 90-minute dynamic [18F]FLT PET/CT. Organs were harvested from independent cohorts for gamma counting, ultrasound scanning, and western blotting. [18F]FLT uptake was significantly greater in 14- (n = 5) and 28-day (n = 3) AAA than in saline control aortae (n = 5) (P 18F]FLT uptake in 14-day AAA (n = 9) compared to saline-infused aortae (n = 4) (P r = 0.71, P n = 3 each) (all P Conclusions [18F]FLT uptake is increased during the active growth phase of the AAA model compared to saline control mice and late-stage AAA.
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- 2019
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49. The value of MR textural analysis in prostate cancer
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Andrew Scarsbrook, N. Patel, and Ann Henry
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Male ,medicine.medical_specialty ,Future studies ,medicine.diagnostic_test ,business.industry ,Prostate ,Normal tissue ,Prostatic Neoplasms ,Magnetic resonance imaging ,General Medicine ,medicine.disease ,Magnetic Resonance Imaging ,Clinical Practice ,Prostate cancer ,medicine.anatomical_structure ,Image Interpretation, Computer-Assisted ,medicine ,Clinical validity ,Humans ,Radiology, Nuclear Medicine and imaging ,Medical physics ,business ,Grading (tumors) - Abstract
Current diagnosis and treatment stratification of patients with suspected prostate cancer relies on a combination of histological and magnetic resonance imaging (MRI) findings. The aim of this article is to provide a brief overview of prostate pathological grading as well as the relevant aspects of multiparametric (MRI) mpMRI, before indicating the potential that magnetic resonance textural analysis (MRTA) offers within prostate cancer. A review of the evidence base on MRTA in prostate cancer will enable discussion of the utility of this field while also indicating recommendations to future research. Radiomic textural analysis allows the assessment of spatial inter-relationships between pixels within an image by use of mathematical methods. First-order textural analysis is better understood and may have more clinical validity than higher-order textural features. Textural features extracted from apparent diffusion coefficient maps have shown the most potential for clinical utility in MRTA of prostate cancers. Future studies should aim to integrate machine learning techniques to better represent the role of MRTA in prostate cancer clinical practice. Nomenclature should be used to reduce misidentification between first-order and second-order energy and entropy. Automated methods of segmentation should be encouraged in order to reduce problems associated with inclusion of normal tissue within regions of interest. The retrospective and small-scale nature of most published studies, make it difficult to draw meaningful conclusions. Future larger prospective studies are required to validate the textural features indicated to have potential in characterisation and/or diagnosis of prostate cancer before translation into routine clinical practice.
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- 2019
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50. Accuracy of Response Assessment Positron Emission Tomography-Computed Tomography Following Definitive Radiotherapy Without Chemotherapy for Head and Neck Squamous Cell Carcinoma
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Andrew Scarsbrook, Mehmet Sen, Moses Arunsingh, Robin Prestwich, Karen Dyker, and S. Vaidyanathan
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Adult ,Male ,medicine.medical_specialty ,medicine.medical_treatment ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,Positron Emission Tomography Computed Tomography ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Positron emission ,Aged ,Retrospective Studies ,PET-CT ,Chemotherapy ,Squamous Cell Carcinoma of Head and Neck ,business.industry ,Head and neck cancer ,Retrospective cohort study ,Middle Aged ,medicine.disease ,Head and neck squamous-cell carcinoma ,Radiation therapy ,Oncology ,030220 oncology & carcinogenesis ,Female ,Radiology ,business ,Chemoradiotherapy - Abstract
Aim There are few data to inform on the use of response assessment 2-[fluorine-18]-fluoro-2-deoxy- d -glucose (FDG) positron emission tomography-computed tomography (PET-CT) following radical radiotherapy without chemotherapy for head and neck squamous cell carcinoma (HNSCC). This retrospective study evaluated the accuracy of PET-CT in HNSCC following radical radiotherapy. Materials and methods In total, 138 patients with HNSCC treated with radical radiotherapy without chemotherapy who underwent a baseline and response assessment FDG PET-CT were identified. FDG PET-CT outcomes were analysed with reference to clinicopathological outcomes. Results The median follow-up was 26 months. FDG-avid disease at baseline was present for the primary site and lymph nodes in 118 and 86 patients, respectively. With regard to the primary tumour, the negative predictive value (NPV) of a complete metabolic response (CMR) was 95%; the positive predictive value (PPV) of equivocal uptake and a positive scan were 6% and 82%, respectively. The likelihood ratios for a CMR, equivocal and positive scans of the primary site were 0.19, 0.22, 14.8, respectively. With regard to lymph node disease, the NPV of a CMR was 91%, the PPV of equivocal uptake and a positive scan were 33% and 88%, respectively. Likelihood ratios for lymph node disease for CMR, equivocal and positive scans were 0.19, 0.97 and 15.1, respectively. Conclusion Compared with the accuracy reported in the literature following chemoradiotherapy, response assessment FDG PET-CT following radical radiotherapy without chemotherapy had a similarly high NPV, whereas the PPV following a positive scan was higher.
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- 2019
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